Package evaluation of CAOS on Julia 1.10.9 (96dc2d8c45*) started at 2025-06-06T14:44:18.753


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 5.14s


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

Installing CAOS...
   Resolving package versions...
    Updating `~/.julia/environments/v1.10/Project.toml`
  [84b91ece] + CAOS v0.1.2
    Updating `~/.julia/environments/v1.10/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 v1.2.1
  [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
  [2a0f44e3] + Base64
  [ade2ca70] + Dates
  [b77e0a4c] + InteractiveUtils
  [8f399da3] + Libdl
  [37e2e46d] + LinearAlgebra
  [56ddb016] + Logging
  [d6f4376e] + Markdown
  [a63ad114] + Mmap
  [de0858da] + Printf
  [9a3f8284] + Random
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization
  [fa267f1f] + TOML v1.0.3
  [8dfed614] + Test
  [cf7118a7] + UUIDs
  [4ec0a83e] + Unicode
  [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0
  [4536629a] + OpenBLAS_jll v0.3.23+4
  [83775a58] + Zlib_jll v1.2.13+1
  [8e850b90] + libblastrampoline_jll v5.11.0+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 7.0s


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

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 16.41s


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

     Testing CAOS
      Status `/tmp/jl_wROgi7/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
      Status `/tmp/jl_wROgi7/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 v1.2.1
  [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
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [b77e0a4c] InteractiveUtils
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [de0858da] Printf
  [9a3f8284] Random
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization
  [fa267f1f] TOML v1.0.3
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
  [e66e0078] CompilerSupportLibraries_jll v1.1.1+0
  [4536629a] OpenBLAS_jll v0.3.23+4
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.11.0+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  3.7s
-----------------------------------------
       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::Vector{Union{RawFD, IO}})
      @ Base ./process.jl:128
    [2] #786
      @ ./process.jl:139 [inlined]
    [3] setup_stdios(f::Base.var"#786#787"{Cmd}, stdios::Vector{Union{RawFD, IO}})
      @ Base ./process.jl:223
    [4] _spawn
      @ ./process.jl:138 [inlined]
    [5] run(::Cmd; wait::Bool)
      @ Base ./process.jl:479
    [6] run
      @ ./process.jl:477 [inlined]
    [7] generate_caos_rules(tree_file_path::String, output_directory::String; protein::Bool)
      @ CAOS ~/.julia/packages/CAOS/6lJsa/src/user_functions.jl:48
    [8] generate_caos_rules(tree_file_path::String, output_directory::String)
      @ CAOS ~/.julia/packages/CAOS/6lJsa/src/user_functions.jl:11
    [9] macro expansion
      @ ~/.julia/packages/CAOS/6lJsa/test/classification.jl:3 [inlined]
   [10] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined]
   [11] top-level scope
      @ ~/.julia/packages/CAOS/6lJsa/test/classification.jl:3
   [12] include(mod::Module, _path::String)
      @ Base ./Base.jl:495
   [13] include(x::String)
      @ Main.TestCAOS ~/.julia/packages/CAOS/6lJsa/test/runtests.jl:1
   [14] top-level scope
      @ ~/.julia/packages/CAOS/6lJsa/test/runtests.jl:21
   [15] include(fname::String)
      @ Base.MainInclude ./client.jl:494
   [16] top-level scope
      @ none:6
   [17] eval
      @ ./boot.jl:385 [inlined]
   [18] exec_options(opts::Base.JLOptions)
      @ Base ./client.jl:296
   [19] _start()
      @ Base ./client.jl:557
Test Summary:  | Error  Total   Time
classification |     1      1  13.1s
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 27.88s

ERROR: LoadError: Package CAOS 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 69.22s: package tests unexpectedly errored