Package evaluation of CAOS on Julia 1.12.0-rc1.2 (995ff9db19*) started at 2025-07-14T14:34:53.181


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 8.9s


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

Installing CAOS...
   Resolving package versions...
    Updating `~/.julia/environments/v1.12/Project.toml`
  [84b91ece] + CAOS v0.1.2
    Updating `~/.julia/environments/v1.12/Manifest.toml`
⌅ [67c07d97] + Automa v0.7.0
  [28d598bf] + BGZFStreams v0.3.2
⌅ [00701ae9] + BioAlignments v1.0.1
  [37cfa864] + BioCore v2.0.5
⌅ [7e6ae17a] + BioSequences v1.1.0
⌅ [3c28c6f8] + BioSymbols v3.1.0
  [fa51a905] + BioTools v1.2.0
  [e1450e63] + BufferedStreams v1.2.2
  [84b91ece] + CAOS v0.1.2
  [944b1d66] + CodecZlib v0.7.8
⌅ [3da002f7] + ColorTypes v0.9.1
⌅ [861a8166] + Combinatorics v0.7.0
⌅ [864edb3b] + DataStructures v0.17.20
  [8f5d6c58] + EzXML v1.2.1
  [a0c94c4b] + FastaIO v1.1.0
⌅ [53c48c17] + FixedPointNumbers v0.7.1
  [92fee26a] + GZip v0.6.2
⌅ [899a7d2d] + GenomicFeatures v1.0.4
  [1cb3b9ac] + IndexableBitVectors v1.0.0
  [524e6230] + IntervalTrees v1.1.0
  [692b3bcd] + JLLWrappers v1.7.0
  [682c06a0] + JSON v0.21.4
  [2ec943e9] + Libz v1.0.1
  [bac558e1] + OrderedCollections v1.8.1
  [69de0a69] + Parsers v2.8.3
⌅ [f27b6e38] + Polynomials v0.6.1
  [aea7be01] + PrecompileTools v1.3.2
  [21216c6a] + Preferences v1.4.3
⌅ [3cdcf5f2] + RecipesBase v0.8.0
  [69024149] + StringEncodings v0.3.7
  [0796e94c] + Tokenize v0.5.29
⌅ [3bb67fe8] + TranscodingStreams v0.9.13
  [7200193e] + Twiddle v1.1.2
  [30578b45] + URIParser v0.4.1
  [ddb6d928] + YAML v0.4.14
  [94ce4f54] + Libiconv_jll v1.18.0+0
⌅ [02c8fc9c] + XML2_jll v2.13.6+1
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates v1.11.0
  [b77e0a4c] + InteractiveUtils v1.11.0
  [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.12.0
  [56ddb016] + Logging v1.11.0
  [d6f4376e] + Markdown v1.11.0
  [a63ad114] + Mmap v1.11.0
  [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
  [8dfed614] + Test v1.11.0
  [cf7118a7] + UUIDs v1.11.0
  [4ec0a83e] + Unicode v1.11.0
  [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [83775a58] + Zlib_jll v1.3.1+2
  [8e850b90] + libblastrampoline_jll v5.13.1+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 4.36s


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

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 22.37s


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

     Testing CAOS
      Status `/tmp/jl_7DNaZV/Project.toml`
⌅ [00701ae9] BioAlignments v1.0.1
⌅ [7e6ae17a] BioSequences v1.1.0
  [fa51a905] BioTools v1.2.0
  [84b91ece] CAOS v0.1.2
  [a0c94c4b] FastaIO v1.1.0
  [682c06a0] JSON v0.21.4
  [0796e94c] Tokenize v0.5.29
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_7DNaZV/Manifest.toml`
⌅ [67c07d97] Automa v0.7.0
  [28d598bf] BGZFStreams v0.3.2
⌅ [00701ae9] BioAlignments v1.0.1
  [37cfa864] BioCore v2.0.5
⌅ [7e6ae17a] BioSequences v1.1.0
⌅ [3c28c6f8] BioSymbols v3.1.0
  [fa51a905] BioTools v1.2.0
  [e1450e63] BufferedStreams v1.2.2
  [84b91ece] CAOS v0.1.2
  [944b1d66] CodecZlib v0.7.8
⌅ [3da002f7] ColorTypes v0.9.1
⌅ [861a8166] Combinatorics v0.7.0
⌅ [864edb3b] DataStructures v0.17.20
  [8f5d6c58] EzXML v1.2.1
  [a0c94c4b] FastaIO v1.1.0
⌅ [53c48c17] FixedPointNumbers v0.7.1
  [92fee26a] GZip v0.6.2
⌅ [899a7d2d] GenomicFeatures v1.0.4
  [1cb3b9ac] IndexableBitVectors v1.0.0
  [524e6230] IntervalTrees v1.1.0
  [692b3bcd] JLLWrappers v1.7.0
  [682c06a0] JSON v0.21.4
  [2ec943e9] Libz v1.0.1
  [bac558e1] OrderedCollections v1.8.1
  [69de0a69] Parsers v2.8.3
⌅ [f27b6e38] Polynomials v0.6.1
  [aea7be01] PrecompileTools v1.3.2
  [21216c6a] Preferences v1.4.3
⌅ [3cdcf5f2] RecipesBase v0.8.0
  [69024149] StringEncodings v0.3.7
  [0796e94c] Tokenize v0.5.29
⌅ [3bb67fe8] TranscodingStreams v0.9.13
  [7200193e] Twiddle v1.1.2
  [30578b45] URIParser v0.4.1
  [ddb6d928] YAML v0.4.14
  [94ce4f54] Libiconv_jll v1.18.0+0
⌅ [02c8fc9c] XML2_jll v2.13.6+1
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.12.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [a63ad114] Mmap v1.11.0
  [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
  [8dfed614] Test v1.11.0
  [cf7118a7] UUIDs v1.11.0
  [4ec0a83e] Unicode v1.11.0
  [e66e0078] CompilerSupportLibraries_jll v1.3.0+1
  [4536629a] OpenBLAS_jll v0.3.29+0
  [83775a58] Zlib_jll v1.3.1+2
  [8e850b90] libblastrampoline_jll v5.13.1+0
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading.
     Testing Running tests...
┌ Warning: This package has been depreceated, and should not be used for new projects. Please see BioTools.jl's repository README for more information.
└ @ BioTools ~/.julia/packages/BioTools/LY7H3/src/BioTools.jl:4
Running tests:
-----------------------------------------
           Testing: Tree functions
Test Summary:  | Pass  Total  Time
tree_functions |   80     80  4.7s
-----------------------------------------
       Testing: Classification
classification: Error During Test at /home/pkgeval/.julia/packages/CAOS/6lJsa/test/classification.jl:1
  Got exception outside of a @test
  IOError: could not spawn `makeblastdb -in data/output/char_labels.fasta -dbtype nucl`: no such file or directory (ENOENT)
  Stacktrace:
    [1] _spawn_primitive(file::String, cmd::Cmd, stdio::Memory{Union{RawFD, Base.SyncCloseFD, IO}})
      @ Base ./process.jl:140
    [2] _spawn
      @ ./process.jl:157 [inlined]
    [3] #_spawn##0
      @ ./process.jl:149 [inlined]
    [4] setup_stdios(f::Base.var"#_spawn##0#_spawn##1"{Cmd}, stdios::Vector{Union{RawFD, Base.FileRedirect, IO}})
      @ Base ./process.jl:236
    [5] _spawn
      @ ./process.jl:148 [inlined]
    [6] run(::Cmd; wait::Bool)
      @ Base ./process.jl:512
    [7] run
      @ ./process.jl:510 [inlined]
    [8] generate_caos_rules(tree_file_path::String, output_directory::String; protein::Bool)
      @ CAOS ~/.julia/packages/CAOS/6lJsa/src/user_functions.jl:48
    [9] generate_caos_rules(tree_file_path::String, output_directory::String)
      @ CAOS ~/.julia/packages/CAOS/6lJsa/src/user_functions.jl:11
   [10] top-level scope
      @ ~/.julia/packages/CAOS/6lJsa/test/classification.jl:3
   [11] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined]
   [12] macro expansion
      @ ~/.julia/packages/CAOS/6lJsa/test/classification.jl:3 [inlined]
   [13] include(mapexpr::Function, mod::Module, _path::String)
      @ Base ./Base.jl:306
   [14] top-level scope
      @ ~/.julia/packages/CAOS/6lJsa/test/runtests.jl:21
   [15] include(mapexpr::Function, mod::Module, _path::String)
      @ Base ./Base.jl:306
   [16] top-level scope
      @ none:6
   [17] eval(m::Module, e::Any)
      @ Core ./boot.jl:489
   [18] exec_options(opts::Base.JLOptions)
      @ Base ./client.jl:287
   [19] _start()
      @ Base ./client.jl:554
Test Summary:  | Error  Total   Time
classification |     1      1  16.8s
RNG of the outermost testset: Random.Xoshiro(0x816b1f9da538567b, 0x8ba50710e594cd8a, 0x22e41b52a1f58ae0, 0xdb520ea48a748cc6, 0xd20d23ed48f24ee3)
ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/CAOS/6lJsa/test/classification.jl:1
in expression starting at /home/pkgeval/.julia/packages/CAOS/6lJsa/test/runtests.jl:1

Testing failed after 33.98s

ERROR: LoadError: Package CAOS 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 93.21s: package tests unexpectedly errored