Package evaluation to load BurrowsWheelerAligner on Julia 1.14.0-DEV.2593 (15c2b67521*) started at 2026-07-03T21:54:22.461


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


Set-up completed after 0.15s


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

Installing BurrowsWheelerAligner...
   Resolving package versions...
   Installed OrderedCollections ──── v1.8.2
   Installed StringViews ─────────── v1.3.7
   Installed CodecZlib ───────────── v0.7.8
   Installed Indexes ─────────────── v0.1.3
   Installed GenomicFeatures ─────── v2.1.0
   Installed BWA_jll ─────────────── v0.7.17+1
   Installed TranscodingStreams ──── v0.9.13
   Installed DataStructures ──────── v0.18.22
   Installed BioGenerics ─────────── v0.1.5
   Installed Twiddle ─────────────── v1.1.2
   Installed BioAlignments ───────── v3.1.0
   Installed Compat ──────────────── v4.18.1
   Installed XAM ─────────────────── v0.4.2
   Installed BioSymbols ──────────── v5.2.0
   Installed BurrowsWheelerAligner ─ v0.1.4
   Installed PrecompileTools ─────── v1.3.4
   Installed JLLWrappers ─────────── v1.8.0
   Installed BGZFStreams ─────────── v0.3.2
   Installed BioSequences ────────── v3.5.1
   Installed FASTX ───────────────── v2.1.7
   Installed IntervalTrees ───────── v1.1.0
   Installed Preferences ─────────── v1.5.2
   Installed Automa ──────────────── v1.2.0
  Installing 1 artifacts
   Installed artifact BWA 460.6 KiB
    Updating `~/.julia/environments/v1.14/Project.toml`
  [231d3afb] + BurrowsWheelerAligner v0.1.4
    Updating `~/.julia/environments/v1.14/Manifest.toml`
  [67c07d97] + Automa v1.2.0
  [28d598bf] + BGZFStreams v0.3.2
  [00701ae9] + BioAlignments v3.1.0
  [47718e42] + BioGenerics v0.1.5
  [7e6ae17a] + BioSequences v3.5.1
  [3c28c6f8] + BioSymbols v5.2.0
  [231d3afb] + BurrowsWheelerAligner v0.1.4
  [944b1d66] + CodecZlib v0.7.8
  [34da2185] + Compat v4.18.1
⌅ [864edb3b] + DataStructures v0.18.22
  [c2308a5c] + FASTX v2.1.7
⌅ [899a7d2d] + GenomicFeatures v2.1.0
⌅ [4ffb77ac] + Indexes v0.1.3
  [524e6230] + IntervalTrees v1.1.0
  [692b3bcd] + JLLWrappers v1.8.0
⌅ [bac558e1] + OrderedCollections v1.8.2
  [aea7be01] + PrecompileTools v1.3.4
  [21216c6a] + Preferences v1.5.2
⌅ [354b36f9] + StringViews v1.3.7
⌅ [3bb67fe8] + TranscodingStreams v0.9.13
  [7200193e] + Twiddle v1.1.2
  [d759349c] + XAM v0.4.2
  [f8ebc3b1] + BWA_jll v0.7.17+1
  [0dad84c5] + ArgTools v1.2.0
  [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 v1.13.0
  [b27032c2] + LibCURL v1.0.0
  [76f85450] + LibGit2 v1.11.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.14.0
  [56ddb016] + Logging v1.11.0
  [d6f4376e] + Markdown v1.11.0
  [ca575930] + NetworkOptions v1.3.0
  [44cfe95a] + Pkg v1.14.0
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v1.13.0
  [9e88b42a] + Serialization v1.11.0
  [f489334b] + StyledStrings v1.13.0
  [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 v1.5.5+2
  [deac9b47] + LibCURL_jll v8.21.0+0
  [e37daf67] + LibGit2_jll v1.9.4+0
  [29816b5a] + LibSSH2_jll v1.11.101+0
  [14a3606d] + MozillaCACerts_jll v2026.5.14
  [4536629a] + OpenBLAS_jll v0.3.33+0
  [458c3c95] + OpenSSL_jll v3.5.7+0
  [efcefdf7] + PCRE2_jll v10.47.0+0
  [83775a58] + Zlib_jll v1.3.2+0
  [3161d3a3] + Zstd_jll v1.5.7+1
  [8e850b90] + libblastrampoline_jll v5.15.0+0
  [8e850ede] + nghttp2_jll v1.69.0+0
  [3f19e933] + p7zip_jll v17.8.0+0
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`

Installation completed after 11.96s


################################################################################
# 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 project...
 149.0 s  ✓ OrderedCollections
   0.8 s  ✓ Twiddle
 285.6 s  ✓ StringViews
  93.1 s  ✓ IntervalTrees
   2.0 s  ✓ Compat
  31.3 s  ✓ Preferences
  94.2 s  ✓ TranscodingStreams
   0.9 s  ✓ Compat → CompatLinearAlgebraExt
  31.8 s  ✓ JLLWrappers
  31.4 s  ✓ PrecompileTools
  56.5 s  ✓ BioGenerics
  38.3 s  ✓ CodecZlib
 276.7 s  ✓ DataStructures
  32.5 s  ✓ BWA_jll
 122.4 s  ✓ BioSymbols
 202.1 s  ✓ Automa
  38.2 s  ✓ BGZFStreams
 193.0 s  ✓ GenomicFeatures
ERROR: LoadError: Creating a new global in closed module `Base` (`##->###0`) breaks incremental compilation because the side effects will not be permanent.
Stacktrace:
  [1] eval_closure_type(mod::Module, closure_type_name::Symbol, field_names::Core.SimpleVector, field_is_box::Core.SimpleVector)
    @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:96
  [2] top-level scope
    @ ~/.julia/packages/BioSequences/31amM/src/counting.jl:129
  [3] eval(m::Module, e::Any)
    @ Core boot.jl:522
  [4] _eval(mod::Module, iter::Base.JuliaLowering.LoweringIterator{Dict{Symbol, Dict{Int64, Any}}}; soft_scope::Nothing)
    @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/eval.jl:745
  [5] eval(mod::Module, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}}; macro_world::UInt64, soft_scope::Nothing, opts::@Kwargs{expr_compat_mode::Bool})
    @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/eval.jl:718 [inlined]
  [6] top-level scope
    @ ~/.julia/packages/BioSequences/31amM/src/counting.jl:129
  [7] include(mapexpr::Function, mod::Module, _path::String)
    @ Base Base.jl:326
  [8] top-level scope
    @ ~/.julia/packages/BioSequences/31amM/src/BioSequences.jl:225
  [9] include(mod::Module, _path::String)
    @ Base Base.jl:325
 [10] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303
 [11] top-level scope
    @ stdin:5
 [12] eval(m::Module, e::Any)
    @ Core boot.jl:522
 [13] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base loading.jl:3132
 [14] include_string(m::Module, txt::String, fname::String)
    @ Base loading.jl:3142 [inlined]
 [15] exec_options(opts::Base.JLOptions)
    @ Base client.jl:353
 [16] _start()
    @ Base client.jl:596
in expression starting at /home/pkgeval/.julia/packages/BioSequences/31amM/src/counting.jl:129
in expression starting at /home/pkgeval/.julia/packages/BioSequences/31amM/src/BioSequences.jl:8
in expression starting at stdin:5
              ✗ BioSequences
 109.4 s  ✓ FASTX
 136.6 s  ✓ Indexes
ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("7e6ae17a-c86d-528c-b3b9-7f778a29fe59"), "BioSequences") 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:56
  [2] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base loading.jl:2837
  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base loading.jl:2685
  [4] macro expansion
    @ loading.jl:2599 [inlined]
  [5] macro expansion
    @ lock.jl:376 [inlined]
  [6] __require(into::Module, mod::Symbol)
    @ Base loading.jl:2563
  [7] require(into::Module, mod::Symbol)
    @ Base loading.jl:2539 [inlined]
  [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String)
    @ Base module.jl:36 [inlined]
  [9] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)
    @ Base module.jl:111
 [10] eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)
    @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:118
 [11] top-level scope
    @ ~/.julia/packages/BioAlignments/I6ecx/src/BioAlignments.jl:86
 [12] include(mod::Module, _path::String)
    @ Base Base.jl:325
 [13] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303
 [14] top-level scope
    @ stdin:5
 [15] eval(m::Module, e::Any)
    @ Core boot.jl:522
 [16] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base loading.jl:3132
 [17] include_string(m::Module, txt::String, fname::String)
    @ Base loading.jl:3142 [inlined]
 [18] exec_options(opts::Base.JLOptions)
    @ Base client.jl:353
 [19] _start()
    @ Base client.jl:596
in expression starting at /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/BioAlignments.jl:3
in expression starting at stdin:5
              ✗ BioAlignments
ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("7e6ae17a-c86d-528c-b3b9-7f778a29fe59"), "BioSequences") 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:56
  [2] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base loading.jl:2837
  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base loading.jl:2685
  [4] macro expansion
    @ loading.jl:2599 [inlined]
  [5] macro expansion
    @ lock.jl:376 [inlined]
  [6] __require(into::Module, mod::Symbol)
    @ Base loading.jl:2563
  [7] require(into::Module, mod::Symbol)
    @ Base loading.jl:2539 [inlined]
  [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String)
    @ Base module.jl:36 [inlined]
  [9] eval_import_path_all(at::Module, path::Expr, keyword::String)
    @ Base module.jl:60
 [10] _eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr})
    @ Base module.jl:101
 [11] eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr})
    @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:118
 [12] top-level scope
    @ ~/.julia/packages/FASTX/KGKFv/ext/BioSequencesExt.jl:4
 [13] include(mod::Module, _path::String)
    @ Base Base.jl:325
 [14] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303
 [15] top-level scope
    @ stdin:5
 [16] eval(m::Module, e::Any)
    @ Core boot.jl:522
 [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base loading.jl:3132
 [18] include_string(m::Module, txt::String, fname::String)
    @ Base loading.jl:3142 [inlined]
 [19] exec_options(opts::Base.JLOptions)
    @ Base client.jl:353
 [20] _start()
    @ Base client.jl:596
in expression starting at /home/pkgeval/.julia/packages/FASTX/KGKFv/ext/BioSequencesExt.jl:1
in expression starting at stdin:5
              ✗ FASTX → BioSequencesExt
ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("00701ae9-d1dc-5365-b64a-a3a3ebf5695e"), "BioAlignments") 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:56
  [2] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base loading.jl:2837
  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base loading.jl:2685
  [4] macro expansion
    @ loading.jl:2599 [inlined]
  [5] macro expansion
    @ lock.jl:376 [inlined]
  [6] __require(into::Module, mod::Symbol)
    @ Base loading.jl:2563
  [7] require(into::Module, mod::Symbol)
    @ Base loading.jl:2539 [inlined]
  [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String)
    @ Base module.jl:36 [inlined]
  [9] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)
    @ Base module.jl:111
 [10] eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)
    @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:118
 [11] top-level scope
    @ ~/.julia/packages/XAM/gm2PK/src/sam/sam.jl:8
 [12] include(mapexpr::Function, mod::Module, _path::String)
    @ Base Base.jl:326
 [13] top-level scope
    @ ~/.julia/packages/XAM/gm2PK/src/XAM.jl:16
 [14] include(mod::Module, _path::String)
    @ Base Base.jl:325
 [15] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303
 [16] top-level scope
    @ stdin:5
 [17] eval(m::Module, e::Any)
    @ Core boot.jl:522
 [18] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base loading.jl:3132
 [19] include_string(m::Module, txt::String, fname::String)
    @ Base loading.jl:3142 [inlined]
 [20] exec_options(opts::Base.JLOptions)
    @ Base client.jl:353
 [21] _start()
    @ Base client.jl:596
in expression starting at /home/pkgeval/.julia/packages/XAM/gm2PK/src/sam/sam.jl:4
in expression starting at /home/pkgeval/.julia/packages/XAM/gm2PK/src/XAM.jl:1
in expression starting at stdin:5
              ✗ XAM
ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("d759349c-bcba-11e9-07c2-5b90f8f05f7c"), "XAM") 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:56
  [2] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base loading.jl:2837
  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base loading.jl:2685
  [4] macro expansion
    @ loading.jl:2599 [inlined]
  [5] macro expansion
    @ lock.jl:376 [inlined]
  [6] __require(into::Module, mod::Symbol)
    @ Base loading.jl:2563
  [7] require(into::Module, mod::Symbol)
    @ Base loading.jl:2539 [inlined]
  [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String)
    @ Base module.jl:36 [inlined]
  [9] eval_import_path_all(at::Module, path::Expr, keyword::String)
    @ Base module.jl:60
 [10] _eval_using(to::Module, path::Expr, flags::UInt8)
    @ Base module.jl:137 [inlined]
 [11] eval_using(to::Module, path::Expr)
    @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:130
 [12] top-level scope
    @ ~/.julia/packages/BurrowsWheelerAligner/RB6Ad/src/BurrowsWheelerAligner.jl:3
 [13] include(mod::Module, _path::String)
    @ Base Base.jl:325
 [14] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303
 [15] top-level scope
    @ stdin:5
 [16] eval(m::Module, e::Any)
    @ Core boot.jl:522
 [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base loading.jl:3132
 [18] include_string(m::Module, txt::String, fname::String)
    @ Base loading.jl:3142 [inlined]
 [19] exec_options(opts::Base.JLOptions)
    @ Base client.jl:353
 [20] _start()
    @ Base client.jl:596
in expression starting at /home/pkgeval/.julia/packages/BurrowsWheelerAligner/RB6Ad/src/BurrowsWheelerAligner.jl:1
in expression starting at stdin:5
              ✗ BurrowsWheelerAligner
  20 dependencies successfully precompiled in 2114 seconds. 30 already precompiled.

Precompilation completed after 2131.4s


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

Loading BurrowsWheelerAligner...
ERROR: LoadError: Creating a new global in closed module `Base` (`##->###0`) breaks incremental compilation because the side effects will not be permanent.
Stacktrace:
  [1] eval_closure_type(mod::Module, closure_type_name::Symbol, field_names::Core.SimpleVector, field_is_box::Core.SimpleVector)
    @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:96
  [2] top-level scope
    @ ~/.julia/packages/BioSequences/31amM/src/counting.jl:129
  [3] eval(m::Module, e::Any)
    @ Core boot.jl:522
  [4] _eval(mod::Module, iter::Base.JuliaLowering.LoweringIterator{Dict{Symbol, Dict{Int64, Any}}}; soft_scope::Nothing)
    @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/eval.jl:745
  [5] eval(mod::Module, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}}; macro_world::UInt64, soft_scope::Nothing, opts::@Kwargs{expr_compat_mode::Bool})
    @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/eval.jl:718 [inlined]
  [6] top-level scope
    @ ~/.julia/packages/BioSequences/31amM/src/counting.jl:129
  [7] include(mapexpr::Function, mod::Module, _path::String)
    @ Base Base.jl:326
  [8] top-level scope
    @ ~/.julia/packages/BioSequences/31amM/src/BioSequences.jl:225
  [9] include(mod::Module, _path::String)
    @ Base Base.jl:325
 [10] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303
 [11] top-level scope
    @ stdin:5
 [12] eval(m::Module, e::Any)
    @ Core boot.jl:522
 [13] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base loading.jl:3132
 [14] include_string(m::Module, txt::String, fname::String)
    @ Base loading.jl:3142 [inlined]
 [15] exec_options(opts::Base.JLOptions)
    @ Base client.jl:353
 [16] _start()
    @ Base client.jl:596
in expression starting at /home/pkgeval/.julia/packages/BioSequences/31amM/src/counting.jl:129
in expression starting at /home/pkgeval/.julia/packages/BioSequences/31amM/src/BioSequences.jl:8
in expression starting at stdin:5
ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("7e6ae17a-c86d-528c-b3b9-7f778a29fe59"), "BioSequences") 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:56
  [2] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base loading.jl:2837
  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base loading.jl:2685
  [4] macro expansion
    @ loading.jl:2599 [inlined]
  [5] macro expansion
    @ lock.jl:376 [inlined]
  [6] __require(into::Module, mod::Symbol)
    @ Base loading.jl:2563
  [7] require(into::Module, mod::Symbol)
    @ Base loading.jl:2539 [inlined]
  [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String)
    @ Base module.jl:36 [inlined]
  [9] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)
    @ Base module.jl:111
 [10] eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)
    @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:118
 [11] top-level scope
    @ ~/.julia/packages/BioAlignments/I6ecx/src/BioAlignments.jl:86
 [12] include(mod::Module, _path::String)
    @ Base Base.jl:325
 [13] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303
 [14] top-level scope
    @ stdin:5
 [15] eval(m::Module, e::Any)
    @ Core boot.jl:522
 [16] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base loading.jl:3132
 [17] include_string(m::Module, txt::String, fname::String)
    @ Base loading.jl:3142 [inlined]
 [18] exec_options(opts::Base.JLOptions)
    @ Base client.jl:353
 [19] _start()
    @ Base client.jl:596
in expression starting at /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/BioAlignments.jl:3
in expression starting at stdin:5
ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("7e6ae17a-c86d-528c-b3b9-7f778a29fe59"), "BioSequences") 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:56
  [2] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base loading.jl:2837
  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base loading.jl:2685
  [4] macro expansion
    @ loading.jl:2599 [inlined]
  [5] macro expansion
    @ lock.jl:376 [inlined]
  [6] __require(into::Module, mod::Symbol)
    @ Base loading.jl:2563
  [7] require(into::Module, mod::Symbol)
    @ Base loading.jl:2539 [inlined]
  [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String)
    @ Base module.jl:36 [inlined]
  [9] eval_import_path_all(at::Module, path::Expr, keyword::String)
    @ Base module.jl:60
 [10] _eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr})
    @ Base module.jl:101
 [11] eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr})
    @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:118
 [12] top-level scope
    @ ~/.julia/packages/FASTX/KGKFv/ext/BioSequencesExt.jl:4
 [13] include(mod::Module, _path::String)
    @ Base Base.jl:325
 [14] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303
 [15] top-level scope
    @ stdin:5
 [16] eval(m::Module, e::Any)
    @ Core boot.jl:522
 [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base loading.jl:3132
 [18] include_string(m::Module, txt::String, fname::String)
    @ Base loading.jl:3142 [inlined]
 [19] exec_options(opts::Base.JLOptions)
    @ Base client.jl:353
 [20] _start()
    @ Base client.jl:596
in expression starting at /home/pkgeval/.julia/packages/FASTX/KGKFv/ext/BioSequencesExt.jl:1
in expression starting at stdin:5
ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("00701ae9-d1dc-5365-b64a-a3a3ebf5695e"), "BioAlignments") 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:56
  [2] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base loading.jl:2837
  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base loading.jl:2685
  [4] macro expansion
    @ loading.jl:2599 [inlined]
  [5] macro expansion
    @ lock.jl:376 [inlined]
  [6] __require(into::Module, mod::Symbol)
    @ Base loading.jl:2563
  [7] require(into::Module, mod::Symbol)
    @ Base loading.jl:2539 [inlined]
  [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String)
    @ Base module.jl:36 [inlined]
  [9] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)
    @ Base module.jl:111
 [10] eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)
    @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:118
 [11] top-level scope
    @ ~/.julia/packages/XAM/gm2PK/src/sam/sam.jl:8
 [12] include(mapexpr::Function, mod::Module, _path::String)
    @ Base Base.jl:326
 [13] top-level scope
    @ ~/.julia/packages/XAM/gm2PK/src/XAM.jl:16
 [14] include(mod::Module, _path::String)
    @ Base Base.jl:325
 [15] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303
 [16] top-level scope
    @ stdin:5
 [17] eval(m::Module, e::Any)
    @ Core boot.jl:522
 [18] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base loading.jl:3132
 [19] include_string(m::Module, txt::String, fname::String)
    @ Base loading.jl:3142 [inlined]
 [20] exec_options(opts::Base.JLOptions)
    @ Base client.jl:353
 [21] _start()
    @ Base client.jl:596
in expression starting at /home/pkgeval/.julia/packages/XAM/gm2PK/src/sam/sam.jl:4
in expression starting at /home/pkgeval/.julia/packages/XAM/gm2PK/src/XAM.jl:1
in expression starting at stdin:5
ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("d759349c-bcba-11e9-07c2-5b90f8f05f7c"), "XAM") 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:56
  [2] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base loading.jl:2837
  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base loading.jl:2685
  [4] macro expansion
    @ loading.jl:2599 [inlined]
  [5] macro expansion
    @ lock.jl:376 [inlined]
  [6] __require(into::Module, mod::Symbol)
    @ Base loading.jl:2563
  [7] require(into::Module, mod::Symbol)
    @ Base loading.jl:2539 [inlined]
  [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String)
    @ Base module.jl:36 [inlined]
  [9] eval_import_path_all(at::Module, path::Expr, keyword::String)
    @ Base module.jl:60
 [10] _eval_using(to::Module, path::Expr, flags::UInt8)
    @ Base module.jl:137 [inlined]
 [11] eval_using(to::Module, path::Expr)
    @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:130
 [12] top-level scope
    @ ~/.julia/packages/BurrowsWheelerAligner/RB6Ad/src/BurrowsWheelerAligner.jl:3
 [13] include(mod::Module, _path::String)
    @ Base Base.jl:325
 [14] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303
 [15] top-level scope
    @ stdin:5
 [16] eval(m::Module, e::Any)
    @ Core boot.jl:522
 [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base loading.jl:3132
 [18] include_string(m::Module, txt::String, fname::String)
    @ Base loading.jl:3142 [inlined]
 [19] exec_options(opts::Base.JLOptions)
    @ Base client.jl:353
 [20] _start()
    @ Base client.jl:596
in expression starting at /home/pkgeval/.julia/packages/BurrowsWheelerAligner/RB6Ad/src/BurrowsWheelerAligner.jl:1
in expression starting at stdin:5
  5 dependencies had output during precompilation:
┌ BioAlignments
│  ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("7e6ae17a-c86d-528c-b3b9-7f778a29fe59"), "BioSequences") 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:56
│    [2] __require_prelocked(pkg::Base.PkgId, env::String)
│      @ Base loading.jl:2837
│    [3] _require_prelocked(uuidkey::Base.PkgId, env::String)
│      @ Base loading.jl:2685
│    [4] macro expansion
│      @ loading.jl:2599 [inlined]
│    [5] macro expansion
│      @ lock.jl:376 [inlined]
│    [6] __require(into::Module, mod::Symbol)
│      @ Base loading.jl:2563
│    [7] require(into::Module, mod::Symbol)
│      @ Base loading.jl:2539 [inlined]
│    [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String)
│      @ Base module.jl:36 [inlined]
│    [9] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)
│      @ Base module.jl:111
│   [10] eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)
│      @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:118
│   [11] top-level scope
│      @ ~/.julia/packages/BioAlignments/I6ecx/src/BioAlignments.jl:86
│   [12] include(mod::Module, _path::String)
│      @ Base Base.jl:325
│   [13] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303
│   [14] top-level scope
│      @ stdin:5
│   [15] eval(m::Module, e::Any)
│      @ Core boot.jl:522
│   [16] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│      @ Base loading.jl:3132
│   [17] include_string(m::Module, txt::String, fname::String)
│      @ Base loading.jl:3142 [inlined]
│   [18] exec_options(opts::Base.JLOptions)
│      @ Base client.jl:353
│   [19] _start()
│      @ Base client.jl:596
│  in expression starting at /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/BioAlignments.jl:3
│  in expression starting at stdin:5
└  
┌ XAM
│  ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("00701ae9-d1dc-5365-b64a-a3a3ebf5695e"), "BioAlignments") 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:56
│    [2] __require_prelocked(pkg::Base.PkgId, env::String)
│      @ Base loading.jl:2837
│    [3] _require_prelocked(uuidkey::Base.PkgId, env::String)
│      @ Base loading.jl:2685
│    [4] macro expansion
│      @ loading.jl:2599 [inlined]
│    [5] macro expansion
│      @ lock.jl:376 [inlined]
│    [6] __require(into::Module, mod::Symbol)
│      @ Base loading.jl:2563
│    [7] require(into::Module, mod::Symbol)
│      @ Base loading.jl:2539 [inlined]
│    [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String)
│      @ Base module.jl:36 [inlined]
│    [9] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)
│      @ Base module.jl:111
│   [10] eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)
│      @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:118
│   [11] top-level scope
│      @ ~/.julia/packages/XAM/gm2PK/src/sam/sam.jl:8
│   [12] include(mapexpr::Function, mod::Module, _path::String)
│      @ Base Base.jl:326
│   [13] top-level scope
│      @ ~/.julia/packages/XAM/gm2PK/src/XAM.jl:16
│   [14] include(mod::Module, _path::String)
│      @ Base Base.jl:325
│   [15] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303
│   [16] top-level scope
│      @ stdin:5
│   [17] eval(m::Module, e::Any)
│      @ Core boot.jl:522
│   [18] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│      @ Base loading.jl:3132
│   [19] include_string(m::Module, txt::String, fname::String)
│      @ Base loading.jl:3142 [inlined]
│   [20] exec_options(opts::Base.JLOptions)
│      @ Base client.jl:353
│   [21] _start()
│      @ Base client.jl:596
│  in expression starting at /home/pkgeval/.julia/packages/XAM/gm2PK/src/sam/sam.jl:4
│  in expression starting at /home/pkgeval/.julia/packages/XAM/gm2PK/src/XAM.jl:1
│  in expression starting at stdin:5
└  
┌ BurrowsWheelerAligner
│  [Output was shown above]
└  
┌ FASTX → BioSequencesExt
│  ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("7e6ae17a-c86d-528c-b3b9-7f778a29fe59"), "BioSequences") 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:56
│    [2] __require_prelocked(pkg::Base.PkgId, env::String)
│      @ Base loading.jl:2837
│    [3] _require_prelocked(uuidkey::Base.PkgId, env::String)
│      @ Base loading.jl:2685
│    [4] macro expansion
│      @ loading.jl:2599 [inlined]
│    [5] macro expansion
│      @ lock.jl:376 [inlined]
│    [6] __require(into::Module, mod::Symbol)
│      @ Base loading.jl:2563
│    [7] require(into::Module, mod::Symbol)
│      @ Base loading.jl:2539 [inlined]
│    [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String)
│      @ Base module.jl:36 [inlined]
│    [9] eval_import_path_all(at::Module, path::Expr, keyword::String)
│      @ Base module.jl:60
│   [10] _eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr})
│      @ Base module.jl:101
│   [11] eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr})
│      @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:118
│   [12] top-level scope
│      @ ~/.julia/packages/FASTX/KGKFv/ext/BioSequencesExt.jl:4
│   [13] include(mod::Module, _path::String)
│      @ Base Base.jl:325
│   [14] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303
│   [15] top-level scope
│      @ stdin:5
│   [16] eval(m::Module, e::Any)
│      @ Core boot.jl:522
│   [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│      @ Base loading.jl:3132
│   [18] include_string(m::Module, txt::String, fname::String)
│      @ Base loading.jl:3142 [inlined]
│   [19] exec_options(opts::Base.JLOptions)
│      @ Base client.jl:353
│   [20] _start()
│      @ Base client.jl:596
│  in expression starting at /home/pkgeval/.julia/packages/FASTX/KGKFv/ext/BioSequencesExt.jl:1
│  in expression starting at stdin:5
└  
┌ BioSequences
│  ERROR: LoadError: Creating a new global in closed module `Base` (`##->###0`) breaks incremental compilation because the side effects will not be permanent.
│  Stacktrace:
│    [1] eval_closure_type(mod::Module, closure_type_name::Symbol, field_names::Core.SimpleVector, field_is_box::Core.SimpleVector)
│      @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:96
│    [2] top-level scope
│      @ ~/.julia/packages/BioSequences/31amM/src/counting.jl:129
│    [3] eval(m::Module, e::Any)
│      @ Core boot.jl:522
│    [4] _eval(mod::Module, iter::Base.JuliaLowering.LoweringIterator{Dict{Symbol, Dict{Int64, Any}}}; soft_scope::Nothing)
│      @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/eval.jl:745
│    [5] eval(mod::Module, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}}; macro_world::UInt64, soft_scope::Nothing, opts::@Kwargs{expr_compat_mode::Bool})
│      @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/eval.jl:718 [inlined]
│    [6] top-level scope
│      @ ~/.julia/packages/BioSequences/31amM/src/counting.jl:129
│    [7] include(mapexpr::Function, mod::Module, _path::String)
│      @ Base Base.jl:326
│    [8] top-level scope
│      @ ~/.julia/packages/BioSequences/31amM/src/BioSequences.jl:225
│    [9] include(mod::Module, _path::String)
│      @ Base Base.jl:325
│   [10] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303
│   [11] top-level scope
│      @ stdin:5
│   [12] eval(m::Module, e::Any)
│      @ Core boot.jl:522
│   [13] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│      @ Base loading.jl:3132
│   [14] include_string(m::Module, txt::String, fname::String)
│      @ Base loading.jl:3142 [inlined]
│   [15] exec_options(opts::Base.JLOptions)
│      @ Base client.jl:353
│   [16] _start()
│      @ Base client.jl:596
│  in expression starting at /home/pkgeval/.julia/packages/BioSequences/31amM/src/counting.jl:129
│  in expression starting at /home/pkgeval/.julia/packages/BioSequences/31amM/src/BioSequences.jl:8
│  in expression starting at stdin:5
└  
ERROR: The following 5 packages failed to precompile:

BioAlignments 
Failed to precompile BioAlignments [00701ae9-d1dc-5365-b64a-a3a3ebf5695e] to "/home/pkgeval/.julia/compiled/v1.14/BioAlignments/jl_0MSPKF" (ProcessExited(1)).

XAM 
Failed to precompile XAM [d759349c-bcba-11e9-07c2-5b90f8f05f7c] to "/home/pkgeval/.julia/compiled/v1.14/XAM/jl_JcETnx" (ProcessExited(1)).

BurrowsWheelerAligner 
Failed to precompile BurrowsWheelerAligner [231d3afb-1936-45f0-8367-36f73a875095] to "/home/pkgeval/.julia/compiled/v1.14/BurrowsWheelerAligner/jl_ldTgFu" (ProcessExited(1)).

FASTX → BioSequencesExt 
Failed to precompile BioSequencesExt [baf92119-a789-5020-bf37-768157dc338a] to "/home/pkgeval/.julia/compiled/v1.14/BioSequencesExt/jl_I3qEL2" (ProcessExited(1)).

BioSequences 
Failed to precompile BioSequences [7e6ae17a-c86d-528c-b3b9-7f778a29fe59] to "/home/pkgeval/.julia/compiled/v1.14/BioSequences/jl_Oroksk" (ProcessExited(1)).


Loading failed after 195.25s

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

Stacktrace:
 [1] pipeline_error(proc::Base.Process)
   @ Base process.jl:612 [inlined]
 [2] run(::Cmd; wait::Bool)
   @ Base process.jl:525
 [3] run(::Cmd)
   @ Base process.jl:522
 [4] top-level scope
   @ /PkgEval.jl/scripts/evaluate.jl:197
 [5] include(mod::Module, _path::String)
   @ Base Base.jl:325
 [6] exec_options(opts::Base.JLOptions)
   @ Base client.jl:355
 [7] _start()
   @ Base client.jl:596
in expression starting at /PkgEval.jl/scripts/evaluate.jl:188

PkgEval failed after 2380.88s: package fails to precompile