Package evaluation of GeneticVariation on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T10:06:54.458


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 8.79s


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

Installing GeneticVariation...
   Resolving package versions...
    Updating `~/.julia/environments/v1.11/Project.toml`
  [9bc6ac9d] + GeneticVariation v0.4.1
    Updating `~/.julia/environments/v1.11/Manifest.toml`
⌅ [67c07d97] + Automa v0.7.0
  [28d598bf] + BGZFStreams v0.3.2
  [37cfa864] + BioCore v2.0.5
⌅ [7e6ae17a] + BioSequences v1.1.0
⌅ [3c28c6f8] + BioSymbols v3.1.0
  [e1450e63] + BufferedStreams v1.2.2
  [944b1d66] + CodecZlib v0.7.8
⌅ [861a8166] + Combinatorics v0.7.0
  [34da2185] + Compat v4.16.0
  [864edb3b] + DataStructures v0.18.22
  [9bc6ac9d] + GeneticVariation v0.4.1
  [1cb3b9ac] + IndexableBitVectors v1.0.0
  [524e6230] + IntervalTrees v1.1.0
  [692b3bcd] + JLLWrappers v1.7.0
  [bac558e1] + OrderedCollections v1.8.0
⌅ [f27b6e38] + Polynomials v0.6.1
  [21216c6a] + Preferences v1.4.3
⌅ [3cdcf5f2] + RecipesBase v0.8.0
  [69024149] + StringEncodings v0.3.7
⌅ [3bb67fe8] + TranscodingStreams v0.9.13
  [7200193e] + Twiddle v1.1.2
  [ddb6d928] + YAML v0.4.13
  [94ce4f54] + Libiconv_jll v1.18.0+0
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates v1.11.0
  [b77e0a4c] + InteractiveUtils v1.11.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.11.0
  [56ddb016] + Logging v1.11.0
  [d6f4376e] + Markdown v1.11.0
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization 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 v1.1.1+0
  [4536629a] + OpenBLAS_jll v0.3.27+1
  [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 To see why use `status --outdated -m`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 2.66s


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

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 75.64s


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

     Testing GeneticVariation
      Status `/tmp/jl_2bT0DO/Project.toml`
⌅ [67c07d97] Automa v0.7.0
  [28d598bf] BGZFStreams v0.3.2
  [37cfa864] BioCore v2.0.5
⌅ [7e6ae17a] BioSequences v1.1.0
  [e1450e63] BufferedStreams v1.2.2
⌅ [861a8166] Combinatorics v0.7.0
  [9bc6ac9d] GeneticVariation v0.4.1
  [524e6230] IntervalTrees v1.1.0
  [7200193e] Twiddle v1.1.2
  [ddb6d928] YAML v0.4.13
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_2bT0DO/Manifest.toml`
⌅ [67c07d97] Automa v0.7.0
  [28d598bf] BGZFStreams v0.3.2
  [37cfa864] BioCore v2.0.5
⌅ [7e6ae17a] BioSequences v1.1.0
⌅ [3c28c6f8] BioSymbols v3.1.0
  [e1450e63] BufferedStreams v1.2.2
  [944b1d66] CodecZlib v0.7.8
⌅ [861a8166] Combinatorics v0.7.0
  [34da2185] Compat v4.16.0
  [864edb3b] DataStructures v0.18.22
  [9bc6ac9d] GeneticVariation v0.4.1
  [1cb3b9ac] IndexableBitVectors v1.0.0
  [524e6230] IntervalTrees v1.1.0
  [692b3bcd] JLLWrappers v1.7.0
  [bac558e1] OrderedCollections v1.8.0
⌅ [f27b6e38] Polynomials v0.6.1
  [21216c6a] Preferences v1.4.3
⌅ [3cdcf5f2] RecipesBase v0.8.0
  [69024149] StringEncodings v0.3.7
⌅ [3bb67fe8] TranscodingStreams v0.9.13
  [7200193e] Twiddle v1.1.2
  [ddb6d928] YAML v0.4.13
  [94ce4f54] Libiconv_jll v1.18.0+0
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.11.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [de0858da] Printf v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization 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 v1.1.1+0
  [4536629a] OpenBLAS_jll v0.3.27+1
  [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...
Cloning into '/home/pkgeval/.julia/packages/BioCore/YBJvb/BioFmtSpecimens'...
Note: switching to 'v1.0.0-9-ga88ddc9'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at a88ddc9 Merge pull request #29 from jgreener64/mmtf
Test Summary: | Pass  Total   Time
VCF           |  165    165  27.7s
BCF: Error During Test at /home/pkgeval/.julia/packages/GeneticVariation/1wh3b/test/bcf.jl:1
  Got exception outside of a @test
  BGZFStreams.BGZFDataError("invalid gzip identifier")
  Stacktrace:
    [1] bgzferror(message::String)
      @ BGZFStreams ~/.julia/packages/BGZFStreams/aVKm9/src/bgzfstream.jl:360
    [2] read_bgzf_block!(input::IOBuffer, block::Vector{UInt8})
      @ BGZFStreams ~/.julia/packages/BGZFStreams/aVKm9/src/bgzfstream.jl:426
    [3] read_blocks!(stream::BGZFStreams.BGZFStream{IOBuffer})
      @ BGZFStreams ~/.julia/packages/BGZFStreams/aVKm9/src/bgzfstream.jl:382
    [4] ensure_buffered_data
      @ ~/.julia/packages/BGZFStreams/aVKm9/src/bgzfstream.jl:339 [inlined]
    [5] read(stream::BGZFStreams.BGZFStream{IOBuffer}, ::Type{UInt8})
      @ BGZFStreams ~/.julia/packages/BGZFStreams/aVKm9/src/bgzfstream.jl:249
    [6] GeneticVariation.BCF.Reader(input::IOBuffer)
      @ GeneticVariation.BCF ~/.julia/packages/GeneticVariation/1wh3b/src/bcf/reader.jl:25
    [7] macro expansion
      @ ~/.julia/packages/GeneticVariation/1wh3b/test/bcf.jl:81 [inlined]
    [8] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined]
    [9] top-level scope
      @ ~/.julia/packages/GeneticVariation/1wh3b/test/bcf.jl:2
   [10] include(mod::Module, _path::String)
      @ Base ./Base.jl:557
   [11] include(x::String)
      @ Main.TestGeneticVariation ~/.julia/packages/GeneticVariation/1wh3b/test/runtests.jl:1
   [12] top-level scope
      @ ~/.julia/packages/GeneticVariation/1wh3b/test/runtests.jl:25
   [13] include(fname::String)
      @ Main ./sysimg.jl:38
   [14] top-level scope
      @ none:6
   [15] eval
      @ ./boot.jl:430 [inlined]
   [16] exec_options(opts::Base.JLOptions)
      @ Base ./client.jl:296
   [17] _start()
      @ Base ./client.jl:531
Test Summary: | Pass  Error  Total  Time
BCF           |   37      1     38  8.2s
ERROR: LoadError: Some tests did not pass: 37 passed, 0 failed, 1 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/GeneticVariation/1wh3b/test/bcf.jl:1
in expression starting at /home/pkgeval/.julia/packages/GeneticVariation/1wh3b/test/runtests.jl:1

Testing failed after 84.29s

ERROR: LoadError: Package GeneticVariation errored during testing
Stacktrace:
 [1] pkgerror(msg::String)
   @ Pkg.Types /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Types.jl:68
 [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/v1.11/Pkg/src/Operations.jl:2124
 [3] test
   @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2007 [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::IOContext{IO}})
   @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:481
 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd})
   @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:159
 [6] test
   @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined]
 [7] #test#74
   @ /opt/julia/share/julia/stdlib/v1.11/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 183.8s: package tests unexpectedly errored