Package evaluation of BurrowsWheelerAligner on Julia 1.13.0-DEV.449 (8d6b63c3a6*) started at 2025-04-29T01:20:28.426


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


Set-up completed after 0.23s


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

Installing BurrowsWheelerAligner...
   Resolving package versions...
    Updating `~/.julia/environments/v1.13/Project.toml`
  [231d3afb] + BurrowsWheelerAligner v0.1.3
    Updating `~/.julia/environments/v1.13/Manifest.toml`
  [67c07d97] + Automa v1.1.0
  [28d598bf] + BGZFStreams v0.3.2
  [00701ae9] + BioAlignments v3.1.0
  [47718e42] + BioGenerics v0.1.5
  [7e6ae17a] + BioSequences v3.4.1
  [3c28c6f8] + BioSymbols v5.2.0
  [231d3afb] + BurrowsWheelerAligner v0.1.3
  [944b1d66] + CodecZlib v0.7.8
  [34da2185] + Compat v4.16.0
  [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 v1.7.0
  [bac558e1] + OrderedCollections v1.8.0
  [aea7be01] + PrecompileTools v1.3.2
  [21216c6a] + Preferences v1.4.3
  [fdea26ae] + SIMD v3.7.1
  [354b36f9] + StringViews v1.3.4
⌅ [3bb67fe8] + TranscodingStreams v0.9.13
  [7200193e] + Twiddle v1.1.2
  [d759349c] + XAM v0.4.2
  [f8ebc3b1] + BWA_jll v0.7.17+1
  [0dad84c5] + ArgTools v1.1.2
  [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 v0.6.4
  [76f85450] + LibGit2 v1.11.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.12.0
  [56ddb016] + Logging v1.11.0
  [d6f4376e] + Markdown v1.11.0
  [ca575930] + NetworkOptions v1.3.0
  [44cfe95a] + Pkg v1.12.0
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization 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 v8.12.1+1
  [e37daf67] + LibGit2_jll v1.9.0+0
  [29816b5a] + LibSSH2_jll v1.11.3+1
  [14a3606d] + MozillaCACerts_jll v2024.12.31
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [458c3c95] + OpenSSL_jll v3.0.16+0
  [83775a58] + Zlib_jll v1.3.1+2
  [8e850b90] + libblastrampoline_jll v5.12.0+0
  [8e850ede] + nghttp2_jll v1.65.0+0
  [3f19e933] + p7zip_jll v17.5.0+2
        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 5.96s


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

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

Precompiling package dependencies...
Precompiling packages...
   1685.9 ms  ✓ BWA_jll
  22663.8 ms  ✓ FASTX
   4222.3 ms  ✓ FASTX → BioSequencesExt
           ✗ BurrowsWheelerAligner
  3 dependencies successfully precompiled in 41 seconds. 50 already precompiled.

ERROR: LoadError: The following 1 direct dependency failed to precompile:

BurrowsWheelerAligner 

Failed to precompile BurrowsWheelerAligner [231d3afb-1936-45f0-8367-36f73a875095] to "/home/pkgeval/.julia/compiled/v1.13/BurrowsWheelerAligner/jl_Dndlpv" (ProcessExited(1)).
WARNING: Imported binding XAM.refname was undeclared at import time during import to BurrowsWheelerAligner.
WARNING: Imported binding XAM.mappingquality was undeclared at import time during import to BurrowsWheelerAligner.
ERROR: LoadError: invalid method definition in BurrowsWheelerAligner: exported function XAM.refname does not exist
Stacktrace:
 [1] top-level scope
   @ ~/.julia/packages/BurrowsWheelerAligner/ffVKK/src/BurrowsWheelerAligner.jl:57
 [2] include(mod::Module, _path::String)
   @ Base ./Base.jl:303
 [3] 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:2978
 [4] top-level scope
   @ stdin:5
 [5] eval(m::Module, e::Any)
   @ Core ./boot.jl:489
 [6] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
   @ Base ./loading.jl:2824
 [7] include_string
   @ ./loading.jl:2834 [inlined]
 [8] exec_options(opts::Base.JLOptions)
   @ Base ./client.jl:329
 [9] _start()
   @ Base ./client.jl:563
in expression starting at /home/pkgeval/.julia/packages/BurrowsWheelerAligner/ffVKK/src/BurrowsWheelerAligner.jl:1
in expression starting at stdin:
in expression starting at /PkgEval.jl/scripts/precompile.jl:37

Precompilation failed after 49.37s



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

Loading BurrowsWheelerAligner...
Precompiling packages...
Info Given BurrowsWheelerAligner was explicitly requested, output will be shown live 
WARNING: Imported binding XAM.refname was undeclared at import time during import to BurrowsWheelerAligner.
WARNING: Imported binding XAM.mappingquality was undeclared at import time during import to BurrowsWheelerAligner.
ERROR: LoadError: invalid method definition in BurrowsWheelerAligner: exported function XAM.refname does not exist
Stacktrace:
 [1] top-level scope
   @ ~/.julia/packages/BurrowsWheelerAligner/ffVKK/src/BurrowsWheelerAligner.jl:57
 [2] include(mod::Module, _path::String)
   @ Base ./Base.jl:303
 [3] 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:2978
 [4] top-level scope
   @ stdin:5
 [5] eval(m::Module, e::Any)
   @ Core ./boot.jl:489
 [6] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
   @ Base ./loading.jl:2824
 [7] include_string
   @ ./loading.jl:2834 [inlined]
 [8] exec_options(opts::Base.JLOptions)
   @ Base ./client.jl:329
 [9] _start()
   @ Base ./client.jl:563
in expression starting at /home/pkgeval/.julia/packages/BurrowsWheelerAligner/ffVKK/src/BurrowsWheelerAligner.jl:1
in expression starting at stdin:5
           ✗ BurrowsWheelerAligner
  0 dependencies successfully precompiled in 7 seconds. 53 already precompiled.

ERROR: The following 1 direct dependency failed to precompile:

BurrowsWheelerAligner 

Failed to precompile BurrowsWheelerAligner [231d3afb-1936-45f0-8367-36f73a875095] to "/home/pkgeval/.julia/compiled/v1.13/BurrowsWheelerAligner/jl_ydtCZb" (ProcessExited(1)).
WARNING: Imported binding XAM.refname was undeclared at import time during import to BurrowsWheelerAligner.
WARNING: Imported binding XAM.mappingquality was undeclared at import time during import to BurrowsWheelerAligner.
ERROR: LoadError: invalid method definition in BurrowsWheelerAligner: exported function XAM.refname does not exist
Stacktrace:
 [1] top-level scope
   @ ~/.julia/packages/BurrowsWheelerAligner/ffVKK/src/BurrowsWheelerAligner.jl:57
 [2] include(mod::Module, _path::String)
   @ Base ./Base.jl:303
 [3] 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:2978
 [4] top-level scope
   @ stdin:5
 [5] eval(m::Module, e::Any)
   @ Core ./boot.jl:489
 [6] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
   @ Base ./loading.jl:2824
 [7] include_string
   @ ./loading.jl:2834 [inlined]
 [8] exec_options(opts::Base.JLOptions)
   @ Base ./client.jl:329
 [9] _start()
   @ Base ./client.jl:563
in expression starting at /home/pkgeval/.julia/packages/BurrowsWheelerAligner/ffVKK/src/BurrowsWheelerAligner.jl:1
in expression starting at stdin:

Loading failed after 10.3s

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 BurrowsWheelerAligner'`, ProcessExited(1)) [1]

Stacktrace:
 [1] pipeline_error
   @ ./process.jl:602 [inlined]
 [2] run(::Cmd; wait::Bool)
   @ Base ./process.jl:517
 [3] run(::Cmd)
   @ Base ./process.jl:514
 [4] top-level scope
   @ /PkgEval.jl/scripts/evaluate.jl:193
 [5] include(mod::Module, _path::String)
   @ Base ./Base.jl:303
 [6] exec_options(opts::Base.JLOptions)
   @ Base ./client.jl:331
 [7] _start()
   @ Base ./client.jl:563
in expression starting at /PkgEval.jl/scripts/evaluate.jl:184

PkgEval failed after 90.95s: package fails to precompile