Package evaluation of BurrowsWheelerAligner on Julia 1.12.0-DEV.2153 (83dcbd426d*) started at 2025-03-31T10:52:48.475


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 9.64s


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

Installing BurrowsWheelerAligner...
   Resolving package versions...
   Installed SIMD ────────────────── v3.7.1
   Installed BWA_jll ─────────────── v0.7.17+1
   Installed Preferences ─────────── v1.4.3
   Installed Twiddle ─────────────── v1.1.2
   Installed BioGenerics ─────────── v0.1.5
   Installed BioSymbols ──────────── v5.1.3
   Installed GenomicFeatures ─────── v2.1.0
   Installed XAM ─────────────────── v0.4.0
   Installed JLLWrappers ─────────── v1.7.0
   Installed OrderedCollections ──── v1.8.0
   Installed PrecompileTools ─────── v1.3.0
   Installed Indexes ─────────────── v0.1.3
   Installed BGZFStreams ─────────── v0.3.2
   Installed StringViews ─────────── v1.3.4
   Installed DataStructures ──────── v0.18.22
   Installed Compat ──────────────── v4.16.0
   Installed IntervalTrees ───────── v1.1.0
   Installed BioSequences ────────── v3.4.1
   Installed BurrowsWheelerAligner ─ v0.1.3
   Installed TranscodingStreams ──── v0.9.13
   Installed CodecZlib ───────────── v0.7.8
   Installed BioAlignments ───────── v3.1.0
   Installed Automa ──────────────── v1.1.0
   Installed FASTX ───────────────── v2.1.7
  Installing 1 artifacts
   Installed artifact BWA 530.2 KiB
    Updating `~/.julia/environments/v1.12/Project.toml`
  [231d3afb] + BurrowsWheelerAligner v0.1.3
    Updating `~/.julia/environments/v1.12/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 v5.1.3
  [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 v1.3.0
  [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 v0.4.0
  [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 v1.6.0
  [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 v8.11.1+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 v1.64.0+1
  [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 6.19s


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

Precompiling PkgEval dependencies...
Precompiling packages...
   7140.3 ms  ✓ TestEnv
  1 dependency successfully precompiled in 9 seconds. 25 already precompiled.

Precompiling package dependencies...
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/v1.12/BurrowsWheelerAligner/jl_KYjGOi".
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:3015
 [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:2861
 [7] include_string
   @ ./loading.jl:2871 [inlined]
 [8] exec_options(opts::Base.JLOptions)
   @ Base ./client.jl:326
 [9] _start()
   @ Base ./client.jl:560
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 177.99s



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

     Testing BurrowsWheelerAligner
      Status `/tmp/jl_8nUw1r/Project.toml`
  [231d3afb] BurrowsWheelerAligner v0.1.3
  [c2308a5c] FASTX v2.1.7
  [d759349c] XAM v0.4.0
  [f8ebc3b1] BWA_jll v0.7.17+1
  [de0858da] Printf v1.11.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_8nUw1r/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 v5.1.3
  [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 v1.3.0
  [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 v0.4.0
  [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 v1.6.0
  [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 v8.11.1+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 v1.64.0+1
  [3f19e933] p7zip_jll v17.5.0+2
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading.
     Testing Running tests...
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:3015
 [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:2861
 [7] include_string
   @ ./loading.jl:2871 [inlined]
 [8] exec_options(opts::Base.JLOptions)
   @ Base ./client.jl:326
 [9] _start()
   @ Base ./client.jl:560
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 8 seconds. 53 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/v1.12/BurrowsWheelerAligner/jl_c80C3w".
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:3015
 [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:2861
 [7] include_string
   @ ./loading.jl:2871 [inlined]
 [8] exec_options(opts::Base.JLOptions)
   @ Base ./client.jl:326
 [9] _start()
   @ Base ./client.jl:560
in expression starting at /home/pkgeval/.julia/packages/BurrowsWheelerAligner/ffVKK/src/BurrowsWheelerAligner.jl:1
in expression starting at stdin:
in expression starting at /home/pkgeval/.julia/packages/BurrowsWheelerAligner/ffVKK/test/runtests.jl:1

Testing failed after 15.55s

ERROR: LoadError: Package BurrowsWheelerAligner errored during testing
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/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/v1.12/Pkg/src/Operations.jl:2365
  [3] test
    @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2220 [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/v1.12/Pkg/src/API.jl:486
  [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:164
  [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:152
  [7] test
    @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 [inlined]
  [8] #test#81
    @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:151 [inlined]
  [9] top-level scope
    @ /PkgEval.jl/scripts/evaluate.jl:219
 [10] include(mod::Module, _path::String)
    @ Base ./Base.jl:303
 [11] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:328
 [12] _start()
    @ Base ./client.jl:560
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

PkgEval failed after 393.24s: package fails to precompile