Package evaluation of GeneFinder on Julia 1.10.9 (96dc2d8c45*) started at 2025-06-06T13:24:09.392


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 5.19s


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

Installing GeneFinder...
   Resolving package versions...
    Updating `~/.julia/environments/v1.10/Project.toml`
  [2bc6ee46] + GeneFinder v0.7.0
    Updating `~/.julia/environments/v1.10/Manifest.toml`
  [47718e42] + BioGenerics v0.1.5
  [f861b655] + BioMarkovChains v1.0.0
  [7e6ae17a] + BioSequences v3.4.1
  [3c28c6f8] + BioSymbols v5.2.0
  [34da2185] + Compat v4.16.0
  [864edb3b] + DataStructures v0.18.22
  [2bc6ee46] + GeneFinder v0.7.0
  [899a7d2d] + GenomicFeatures v3.0.0
  [524e6230] + IntervalTrees v1.1.0
  [c8e1da08] + IterTools v1.10.0
  [bac558e1] + OrderedCollections v1.8.1
⌅ [aea7be01] + PrecompileTools v1.2.1
  [21216c6a] + Preferences v1.4.3
  [1e83bf80] + StaticArraysCore v1.4.3
  [3bb67fe8] + TranscodingStreams v0.11.3
  [7200193e] + Twiddle v1.1.2
  [2ef45bd6] + VectorizedKmers v0.9.2
  [2a0f44e3] + Base64
  [ade2ca70] + Dates
  [b77e0a4c] + InteractiveUtils
  [d6f4376e] + Markdown
  [de0858da] + Printf
  [9a3f8284] + Random
  [ea8e919c] + SHA v0.7.0
  [fa267f1f] + TOML v1.0.3
  [cf7118a7] + UUIDs
  [4ec0a83e] + Unicode
        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 To see why use `status --outdated -m`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 7.89s


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

Precompiling PkgEval dependencies...

Precompiling package dependencies...
ERROR: LoadError: The following 1 direct dependency failed to precompile:

GeneFinder 

Failed to precompile GeneFinder [2bc6ee46-2158-4f5a-a720-91cb2d7cee64] to "/home/pkgeval/.julia/compiled/v1.10/GeneFinder/jl_IBuOHl".
ERROR: LoadError: UndefVarError: `public` not defined
Stacktrace:
 [1] top-level scope
   @ :0
 [2] include(mod::Module, _path::String)
   @ Base ./Base.jl:495
 [3] include(x::String)
   @ GeneFinder ~/.julia/packages/GeneFinder/HqAdA/src/GeneFinder.jl:1
 [4] top-level scope
   @ ~/.julia/packages/GeneFinder/HqAdA/src/GeneFinder.jl:47
 [5] include
   @ ./Base.jl:495 [inlined]
 [6] 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:2292
 [7] top-level scope
   @ stdin:4
in expression starting at /home/pkgeval/.julia/packages/GeneFinder/HqAdA/src/rbs.jl:2
in expression starting at /home/pkgeval/.julia/packages/GeneFinder/HqAdA/src/GeneFinder.jl:1
in expression starting at stdin:
in expression starting at /PkgEval.jl/scripts/precompile.jl:37

Precompilation failed after 23.2s



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

     Testing GeneFinder
      Status `/tmp/jl_y6uHx3/Project.toml`
  [4c88cf16] Aqua v0.8.13
  [f861b655] BioMarkovChains v1.0.0
  [7e6ae17a] BioSequences v3.4.1
  [c2308a5c] FASTX v2.1.7
  [2bc6ee46] GeneFinder v0.7.0
  [899a7d2d] GenomicFeatures v3.0.0
  [f8b46487] TestItemRunner v1.1.0
  [1c621080] TestItems v1.0.0
  [8dfed614] Test
      Status `/tmp/jl_y6uHx3/Manifest.toml`
  [4c88cf16] Aqua v0.8.13
  [67c07d97] Automa v1.1.0
  [47718e42] BioGenerics v0.1.5
  [f861b655] BioMarkovChains v1.0.0
  [7e6ae17a] BioSequences v3.4.1
  [3c28c6f8] BioSymbols v5.2.0
  [34da2185] Compat v4.16.0
  [864edb3b] DataStructures v0.18.22
  [c2308a5c] FASTX v2.1.7
  [2bc6ee46] GeneFinder v0.7.0
  [899a7d2d] GenomicFeatures v3.0.0
  [524e6230] IntervalTrees v1.1.0
  [c8e1da08] IterTools v1.10.0
  [bac558e1] OrderedCollections v1.8.1
⌅ [aea7be01] PrecompileTools v1.2.1
  [21216c6a] Preferences v1.4.3
  [fdea26ae] SIMD v3.7.1
  [1e83bf80] StaticArraysCore v1.4.3
  [354b36f9] StringViews v1.3.4
  [f8b46487] TestItemRunner v1.1.0
  [1c621080] TestItems v1.0.0
  [3bb67fe8] TranscodingStreams v0.11.3
  [7200193e] Twiddle v1.1.2
  [2ef45bd6] VectorizedKmers v0.9.2
  [0dad84c5] ArgTools v1.1.1
  [56f22d72] Artifacts
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching
  [b77e0a4c] InteractiveUtils
  [b27032c2] LibCURL v0.6.4
  [76f85450] LibGit2
  [8f399da3] Libdl
  [56ddb016] Logging
  [d6f4376e] Markdown
  [ca575930] NetworkOptions v1.2.0
  [44cfe95a] Pkg v1.10.0
  [de0858da] Printf
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization
  [6462fe0b] Sockets
  [fa267f1f] TOML v1.0.3
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
  [deac9b47] LibCURL_jll v8.4.0+0
  [e37daf67] LibGit2_jll v1.6.4+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.2+1
  [14a3606d] MozillaCACerts_jll v2023.1.10
  [83775a58] Zlib_jll v1.2.13+1
  [8e850ede] nghttp2_jll v1.52.0+1
  [3f19e933] p7zip_jll v17.4.0+2
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading.
     Testing Running tests...
ERROR: LoadError: UndefVarError: `public` not defined
Stacktrace:
 [1] top-level scope
   @ :0
 [2] include(mod::Module, _path::String)
   @ Base ./Base.jl:495
 [3] include(x::String)
   @ GeneFinder ~/.julia/packages/GeneFinder/HqAdA/src/GeneFinder.jl:1
 [4] top-level scope
   @ ~/.julia/packages/GeneFinder/HqAdA/src/GeneFinder.jl:47
 [5] include
   @ ./Base.jl:495 [inlined]
 [6] 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::String)
   @ Base ./loading.jl:2292
 [7] top-level scope
   @ stdin:4
in expression starting at /home/pkgeval/.julia/packages/GeneFinder/HqAdA/src/rbs.jl:2
in expression starting at /home/pkgeval/.julia/packages/GeneFinder/HqAdA/src/GeneFinder.jl:1
in expression starting at stdin:4
ERROR: LoadError: Failed to precompile GeneFinder [2bc6ee46-2158-4f5a-a720-91cb2d7cee64] to "/home/pkgeval/.julia/compiled/v1.10/GeneFinder/jl_cK9VWo".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
    @ Base ./loading.jl:2539
  [3] compilecache
    @ ./loading.jl:2411 [inlined]
  [4] (::Base.var"#971#972"{Base.PkgId})()
    @ Base ./loading.jl:2044
  [5] mkpidlock(f::Base.var"#971#972"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:93
  [6] #mkpidlock#6
    @ /opt/julia/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:88 [inlined]
  [7] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:111
  [8] #invokelatest#2
    @ ./essentials.jl:894 [inlined]
  [9] invokelatest
    @ ./essentials.jl:889 [inlined]
 [10] maybe_cachefile_lock(f::Base.var"#971#972"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3054
 [11] maybe_cachefile_lock
    @ ./loading.jl:3051 [inlined]
 [12] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2040
 [13] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1882
 [14] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [15] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [16] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1873
 [17] macro expansion
    @ ./loading.jl:1860 [inlined]
 [18] macro expansion
    @ ./lock.jl:267 [inlined]
 [19] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1823
 [20] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [21] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [22] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1816
 [23] include(fname::String)
    @ Base.MainInclude ./client.jl:494
 [24] top-level scope
    @ none:6
in expression starting at /home/pkgeval/.julia/packages/GeneFinder/HqAdA/test/runtests.jl:1

Testing failed after 14.8s

ERROR: LoadError: Package GeneFinder errored during testing
Stacktrace:
 [1] pkgerror(msg::String)
   @ Pkg.Types /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70
 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.10/Pkg/src/Operations.jl:2034
 [3] test
   @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1915 [inlined]
 [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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::Base.PipeEndpoint})
   @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:444
 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.PipeEndpoint, kwargs::@Kwargs{julia_args::Cmd})
   @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:159
 [6] test
   @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined]
 [7] #test#74
   @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined]
 [8] top-level scope
   @ /PkgEval.jl/scripts/evaluate.jl:219
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

PkgEval failed after 65.53s: package fails to precompile