Package evaluation of GeneFinder on Julia 1.12.0-rc1.2 (995ff9db19*) started at 2025-07-14T12:52:08.569


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 9.06s


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

Installing GeneFinder...
   Resolving package versions...
    Updating `~/.julia/environments/v1.12/Project.toml`
  [2bc6ee46] + GeneFinder v0.7.0
    Updating `~/.julia/environments/v1.12/Manifest.toml`
  [47718e42] + BioGenerics v0.1.5
  [f861b655] + BioMarkovChains v1.0.0
  [7e6ae17a] + BioSequences v3.4.2
  [3c28c6f8] + BioSymbols v5.2.0
  [34da2185] + Compat v4.17.0
  [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 v1.3.2
  [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 v1.11.0
  [ade2ca70] + Dates v1.11.0
  [b77e0a4c] + InteractiveUtils v1.11.0
  [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0
  [d6f4376e] + Markdown v1.11.0
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v0.7.0
  [f489334b] + StyledStrings v1.11.0
  [fa267f1f] + TOML v1.0.3
  [cf7118a7] + UUIDs v1.11.0
  [4ec0a83e] + Unicode v1.11.0

Installation completed after 3.63s


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# Precompilation
#

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 27.8s


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# Testing
#

     Testing GeneFinder
      Status `/tmp/jl_VU51Ri/Project.toml`
  [4c88cf16] Aqua v0.8.13
  [f861b655] BioMarkovChains v1.0.0
  [7e6ae17a] BioSequences v3.4.2
  [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 v1.11.0
      Status `/tmp/jl_VU51Ri/Manifest.toml`
  [4c88cf16] Aqua v0.8.13
  [67c07d97] Automa v1.1.0
  [47718e42] BioGenerics v0.1.5
  [f861b655] BioMarkovChains v1.0.0
  [7e6ae17a] BioSequences v3.4.2
  [3c28c6f8] BioSymbols v5.2.0
  [34da2185] Compat v4.17.0
  [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 v1.3.2
  [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 v1.1.2
  [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
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [ca575930] NetworkOptions v1.3.0
  [44cfe95a] Pkg v1.13.0
  [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
  [deac9b47] LibCURL_jll v8.11.1+1
  [e37daf67] LibGit2_jll v1.9.0+0
  [29816b5a] LibSSH2_jll v1.11.3+1
  [14a3606d] MozillaCACerts_jll v2025.5.20
  [458c3c95] OpenSSL_jll v3.5.1+0
  [83775a58] Zlib_jll v1.3.1+2
  [8e850ede] nghttp2_jll v1.64.0+1
  [3f19e933] p7zip_jll v17.5.0+2
     Testing Running tests...
Precompiling packages...
Info Given GenomicFeatures was explicitly requested, output will be shown live 
WARNING: method definition for == at /home/pkgeval/.julia/packages/GenomicFeatures/tOEn1/src/position.jl:57 declares type variable T but does not use it.
   2039.9 ms  ✓ GenomicFeatures
  1 dependency successfully precompiled in 2 seconds. 16 already precompiled.
  1 dependency had output during precompilation:
┌ GenomicFeatures
│  [Output was shown above]
└  
Precompiling packages...
   6093.5 ms  ✓ GeneFinder
  1 dependency successfully precompiled in 6 seconds. 27 already precompiled.
ERROR: LoadError: SystemError: opening file "data/out-seq.fna": Permission denied
Stacktrace:
  [1] systemerror(p::String, errno::Int32; extrainfo::Nothing)
    @ Base ./error.jl:186
  [2] open(fname::String; lock::Bool, read::Nothing, write::Nothing, create::Nothing, truncate::Bool, append::Nothing)
    @ Base ./iostream.jl:317
  [3] open
    @ ./iostream.jl:296 [inlined]
  [4] open(fname::String, mode::String; lock::Bool)
    @ Base ./iostream.jl:380
  [5] open(fname::String, mode::String)
    @ Base ./iostream.jl:379
  [6] open(::Main.var"##278".var"#2#3", ::String, ::Vararg{String}; kwargs::@Kwargs{})
    @ Base ./io.jl:408
  [7] open(::Function, ::String, ::String)
    @ Base ./io.jl:407
  [8] top-level scope
    @ ~/.julia/packages/GeneFinder/HqAdA/test/iotest.jl:15
  [9] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [10] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2837
 [11] include_string(m::Module, txt::String, fname::String)
    @ Base ./loading.jl:2847
 [12] #run_testitem##6
    @ ~/.julia/packages/TestItemRunner/Q6zqe/src/TestItemRunner.jl:118 [inlined]
 [13] withpath(f::TestItemRunner.var"#run_testitem##6#run_testitem##7"{String, String, Module}, path::String)
    @ TestItemRunner ~/.julia/packages/TestItemRunner/Q6zqe/src/vendored_code.jl:7
 [14] #run_testitem##4
    @ ~/.julia/packages/TestItemRunner/Q6zqe/src/TestItemRunner.jl:117 [inlined]
 [15] cd(f::TestItemRunner.var"#run_testitem##4#run_testitem##5"{String, String, Module}, dir::String)
    @ Base.Filesystem ./file.jl:112
 [16] run_testitem(filepath::String, use_default_usings::Bool, setups::Vector{Symbol}, package_name::String, original_code::String, line::Int64, column::Int64, test_setup_module_set::TestItemRunner.TestSetupModuleSet, testsetups::Dict{Symbol, Any})
    @ TestItemRunner ~/.julia/packages/TestItemRunner/Q6zqe/src/TestItemRunner.jl:116
 [17] run_tests(path::String; filter::Nothing, verbose::Bool)
    @ TestItemRunner ~/.julia/packages/TestItemRunner/Q6zqe/src/TestItemRunner.jl:221
 [18] run_tests(path::String)
    @ TestItemRunner ~/.julia/packages/TestItemRunner/Q6zqe/src/TestItemRunner.jl:133
 [19] top-level scope
    @ ~/.julia/packages/GeneFinder/HqAdA/test/runtests.jl:13
 [20] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:306
 [21] top-level scope
    @ none:6
 [22] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [23] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:287
 [24] _start()
    @ Base ./client.jl:554
in expression starting at /home/pkgeval/.julia/packages/GeneFinder/HqAdA/test/iotest.jl:15
in expression starting at /home/pkgeval/.julia/packages/GeneFinder/HqAdA/test/runtests.jl:1

Testing failed after 72.92s

ERROR: LoadError: Package GeneFinder 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:2458
  [3] test
    @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2313 [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:511
  [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:305
 [11] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:321
 [12] _start()
    @ Base ./client.jl:554
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

PkgEval failed after 134.56s: package tests unexpectedly errored