Package evaluation of PhylogeneticFactorAnalysis on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T18:02:01.769


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 8.33s


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

Installing PhylogeneticFactorAnalysis...
   Resolving package versions...
   Installed Conda ─ v1.10.2
   Installed RCall ─ v0.13.18
    Updating `~/.julia/environments/v1.11/Project.toml`
  [88e69f3b] + PhylogeneticFactorAnalysis v1.0.0
    Updating `~/.julia/environments/v1.11/Manifest.toml`
  [2ff12cca] + BEASTXMLConstructor v1.0.0
  [af749cb1] + BeastUtils v1.0.0
  [a74b3585] + Blosc v0.7.3
  [336ed68f] + CSV v0.10.15
  [324d7699] + CategoricalArrays v0.10.8
  [944b1d66] + CodecZlib v0.7.8
  [861a8166] + Combinatorics v1.0.2
  [34da2185] + Compat v4.16.0
  [8f4d0f93] + Conda v1.10.2
  [a8cc5b0e] + Crayons v4.1.1
  [9a962f9c] + DataAPI v1.16.0
  [a93c6f00] + DataFrames v1.7.0
  [864edb3b] + DataStructures v0.18.22
  [e2d170a0] + DataValueInterfaces v1.0.0
  [8bb1440f] + DelimitedFiles v1.9.1
  [ffbed154] + DocStringExtensions v0.9.4
  [8f5d6c58] + EzXML v1.2.1
  [5789e2e9] + FileIO v1.17.0
  [48062228] + FilePathsBase v0.9.24
  [c8ec2601] + H5Zblosc v0.1.2
  [f67ccb44] + HDF5 v0.17.2
  [34004b35] + HypergeometricFunctions v0.3.28
  [842dd82b] + InlineStrings v1.4.3
  [41ab1584] + InvertedIndices v1.3.1
  [92d709cd] + IrrationalConstants v0.2.4
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [4138dd39] + JLD v0.13.5
  [692b3bcd] + JLLWrappers v1.7.0
  [682c06a0] + JSON v0.21.4
  [b964fa9f] + LaTeXStrings v1.4.0
  [9c8b4983] + LightXML v0.9.1
  [2ab3a3ac] + LogExpFunctions v0.3.29
  [6e857e4b] + MCMCDiagnostics v0.4.0
  [3da0fdf6] + MPIPreferences v0.1.11
  [e1d29d7a] + Missings v1.2.0
  [bac558e1] + OrderedCollections v1.8.0
  [69de0a69] + Parsers v2.8.1
  [88e69f3b] + PhylogeneticFactorAnalysis v1.0.0
  [2dfb63ee] + PooledArrays v1.4.3
⌅ [aea7be01] + PrecompileTools v1.2.1
  [21216c6a] + Preferences v1.4.3
  [08abe8d2] + PrettyTables v2.4.0
⌅ [6f49c342] + RCall v0.13.18
  [189a3867] + Reexport v1.2.2
  [ae029012] + Requires v1.3.1
  [79098fc4] + Rmath v0.8.0
  [91c51154] + SentinelArrays v1.4.8
  [1277b4bf] + ShiftedArrays v2.0.0
  [a2af1166] + SortingAlgorithms v1.2.1
  [276daf66] + SpecialFunctions v2.5.0
  [10745b16] + Statistics v1.11.1
  [82ae8749] + StatsAPI v1.7.0
⌅ [2913bbd2] + StatsBase v0.33.21
  [4c63d2b9] + StatsFuns v1.4.0
  [3eaba693] + StatsModels v0.7.4
  [892a3eda] + StringManipulation v0.4.1
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.0
  [3bb67fe8] + TranscodingStreams v0.11.3
  [3a884ed6] + UnPack v1.0.2
  [81def892] + VersionParsing v1.3.0
  [ea10d353] + WeakRefStrings v1.4.2
  [1b915085] + WinReg v1.0.0
  [76eceee3] + WorkerUtilities v1.6.1
  [0b7ba130] + Blosc_jll v1.21.7+0
  [0234f1f7] + HDF5_jll v1.14.6+0
  [e33a78d0] + Hwloc_jll v2.12.0+0
  [94ce4f54] + Libiconv_jll v1.18.0+0
  [5ced341a] + Lz4_jll v1.10.1+0
  [7cb0a576] + MPICH_jll v4.3.0+1
  [f1f71cc9] + MPItrampoline_jll v5.5.3+0
  [9237b28f] + MicrosoftMPI_jll v10.1.4+3
  [fe0851c0] + OpenMPI_jll v5.0.7+2
  [458c3c95] + OpenSSL_jll v3.0.16+0
  [efe28fd5] + OpenSpecFun_jll v0.5.6+0
  [f50d1b31] + Rmath_jll v0.5.1+0
  [02c8fc9c] + XML2_jll v2.13.6+1
  [3161d3a3] + Zstd_jll v1.5.7+1
  [477f73a3] + libaec_jll v1.1.3+0
  [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
  [9fa8497b] + Future v1.11.0
  [b77e0a4c] + InteractiveUtils v1.11.0
  [4af54fe1] + LazyArtifacts v1.11.0
  [b27032c2] + LibCURL v0.6.4
  [76f85450] + LibGit2 v1.11.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.11.0
  [56ddb016] + Logging v1.11.0
  [d6f4376e] + Markdown v1.11.0
  [a63ad114] + Mmap v1.11.0
  [ca575930] + NetworkOptions v1.2.0
  [44cfe95a] + Pkg v1.11.0
  [de0858da] + Printf v1.11.0
  [3fa0cd96] + REPL v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization v1.11.0
  [6462fe0b] + Sockets v1.11.0
  [2f01184e] + SparseArrays v1.11.0
  [f489334b] + StyledStrings v1.11.0
  [fa267f1f] + TOML v1.0.3
  [a4e569a6] + Tar v1.10.0
  [cf7118a7] + UUIDs v1.11.0
  [4ec0a83e] + Unicode v1.11.0
  [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0
  [deac9b47] + LibCURL_jll v8.6.0+0
  [e37daf67] + LibGit2_jll v1.7.2+0
  [29816b5a] + LibSSH2_jll v1.11.0+1
  [c8ffd9c3] + MbedTLS_jll v2.28.6+0
  [14a3606d] + MozillaCACerts_jll v2023.12.12
  [4536629a] + OpenBLAS_jll v0.3.27+1
  [05823500] + OpenLibm_jll v0.8.5+0
  [bea87d4a] + SuiteSparse_jll v7.7.0+0
  [83775a58] + Zlib_jll v1.2.13+1
  [8e850b90] + libblastrampoline_jll v5.11.0+0
  [8e850ede] + nghttp2_jll v1.59.0+0
  [3f19e933] + p7zip_jll v17.4.0+2
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
    Building Conda → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/b19db3927f0db4151cb86d073689f2428e524576/build.log`
    Building RCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/3084689b18f9e5e817a6ce9a83a7654d8ad0f2f6/build.log`

Installation completed after 114.89s


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# Precompilation
#

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 164.68s


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

     Testing PhylogeneticFactorAnalysis
      Status `/tmp/jl_wuGtIC/Project.toml`
  [2ff12cca] BEASTXMLConstructor v1.0.0
  [af749cb1] BeastUtils v1.0.0
  [336ed68f] CSV v0.10.15
  [861a8166] Combinatorics v1.0.2
  [a93c6f00] DataFrames v1.7.0
  [8f5d6c58] EzXML v1.2.1
  [4138dd39] JLD v0.13.5
  [88e69f3b] PhylogeneticFactorAnalysis v1.0.0
⌅ [6f49c342] RCall v0.13.18
  [1bc83da4] SafeTestsets v0.1.0
  [10745b16] Statistics v1.11.1
  [3a884ed6] UnPack v1.0.2
  [37e2e46d] LinearAlgebra v1.11.0
  [44cfe95a] Pkg v1.11.0
  [9a3f8284] Random v1.11.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_wuGtIC/Manifest.toml`
  [2ff12cca] BEASTXMLConstructor v1.0.0
  [af749cb1] BeastUtils v1.0.0
  [a74b3585] Blosc v0.7.3
  [336ed68f] CSV v0.10.15
  [324d7699] CategoricalArrays v0.10.8
  [944b1d66] CodecZlib v0.7.8
  [861a8166] Combinatorics v1.0.2
  [34da2185] Compat v4.16.0
  [8f4d0f93] Conda v1.10.2
  [a8cc5b0e] Crayons v4.1.1
  [9a962f9c] DataAPI v1.16.0
  [a93c6f00] DataFrames v1.7.0
  [864edb3b] DataStructures v0.18.22
  [e2d170a0] DataValueInterfaces v1.0.0
  [8bb1440f] DelimitedFiles v1.9.1
  [ffbed154] DocStringExtensions v0.9.4
  [8f5d6c58] EzXML v1.2.1
  [5789e2e9] FileIO v1.17.0
  [48062228] FilePathsBase v0.9.24
  [c8ec2601] H5Zblosc v0.1.2
  [f67ccb44] HDF5 v0.17.2
  [34004b35] HypergeometricFunctions v0.3.28
  [842dd82b] InlineStrings v1.4.3
  [41ab1584] InvertedIndices v1.3.1
  [92d709cd] IrrationalConstants v0.2.4
  [82899510] IteratorInterfaceExtensions v1.0.0
  [4138dd39] JLD v0.13.5
  [692b3bcd] JLLWrappers v1.7.0
  [682c06a0] JSON v0.21.4
  [b964fa9f] LaTeXStrings v1.4.0
  [9c8b4983] LightXML v0.9.1
  [2ab3a3ac] LogExpFunctions v0.3.29
  [6e857e4b] MCMCDiagnostics v0.4.0
  [3da0fdf6] MPIPreferences v0.1.11
  [e1d29d7a] Missings v1.2.0
  [bac558e1] OrderedCollections v1.8.0
  [69de0a69] Parsers v2.8.1
  [88e69f3b] PhylogeneticFactorAnalysis v1.0.0
  [2dfb63ee] PooledArrays v1.4.3
⌅ [aea7be01] PrecompileTools v1.2.1
  [21216c6a] Preferences v1.4.3
  [08abe8d2] PrettyTables v2.4.0
⌅ [6f49c342] RCall v0.13.18
  [189a3867] Reexport v1.2.2
  [ae029012] Requires v1.3.1
  [79098fc4] Rmath v0.8.0
  [1bc83da4] SafeTestsets v0.1.0
  [91c51154] SentinelArrays v1.4.8
  [1277b4bf] ShiftedArrays v2.0.0
  [a2af1166] SortingAlgorithms v1.2.1
  [276daf66] SpecialFunctions v2.5.0
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.7.0
⌅ [2913bbd2] StatsBase v0.33.21
  [4c63d2b9] StatsFuns v1.4.0
  [3eaba693] StatsModels v0.7.4
  [892a3eda] StringManipulation v0.4.1
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.0
  [3bb67fe8] TranscodingStreams v0.11.3
  [3a884ed6] UnPack v1.0.2
  [81def892] VersionParsing v1.3.0
  [ea10d353] WeakRefStrings v1.4.2
  [1b915085] WinReg v1.0.0
  [76eceee3] WorkerUtilities v1.6.1
  [0b7ba130] Blosc_jll v1.21.7+0
  [0234f1f7] HDF5_jll v1.14.6+0
  [e33a78d0] Hwloc_jll v2.12.0+0
  [94ce4f54] Libiconv_jll v1.18.0+0
  [5ced341a] Lz4_jll v1.10.1+0
  [7cb0a576] MPICH_jll v4.3.0+1
  [f1f71cc9] MPItrampoline_jll v5.5.3+0
  [9237b28f] MicrosoftMPI_jll v10.1.4+3
  [fe0851c0] OpenMPI_jll v5.0.7+2
  [458c3c95] OpenSSL_jll v3.0.16+0
  [efe28fd5] OpenSpecFun_jll v0.5.6+0
  [f50d1b31] Rmath_jll v0.5.1+0
  [02c8fc9c] XML2_jll v2.13.6+1
  [3161d3a3] Zstd_jll v1.5.7+1
  [477f73a3] libaec_jll v1.1.3+0
  [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
  [9fa8497b] Future v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [4af54fe1] LazyArtifacts v1.11.0
  [b27032c2] LibCURL v0.6.4
  [76f85450] LibGit2 v1.11.0
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.11.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [a63ad114] Mmap v1.11.0
  [ca575930] NetworkOptions v1.2.0
  [44cfe95a] Pkg v1.11.0
  [de0858da] Printf v1.11.0
  [3fa0cd96] REPL v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization v1.11.0
  [6462fe0b] Sockets v1.11.0
  [2f01184e] SparseArrays 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
  [e66e0078] CompilerSupportLibraries_jll v1.1.1+0
  [deac9b47] LibCURL_jll v8.6.0+0
  [e37daf67] LibGit2_jll v1.7.2+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.6+0
  [14a3606d] MozillaCACerts_jll v2023.12.12
  [4536629a] OpenBLAS_jll v0.3.27+1
  [05823500] OpenLibm_jll v0.8.5+0
  [bea87d4a] SuiteSparse_jll v7.7.0+0
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.11.0+0
  [8e850ede] nghttp2_jll v1.59.0+0
  [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...
┌ Warning: MCMCDiagnostics.jl has been deprecated in favor of MCMCDiagnosticTools.jl.
│ (https://github.com/TuringLang/MCMCDiagnosticTools.jl/) and is no longer
│ maintained.
└ @ MCMCDiagnostics ~/.julia/packages/MCMCDiagnostics/uVCwA/src/MCMCDiagnostics.jl:4
Checking Java installation...
PFA test: Error During Test at /home/pkgeval/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:30
  Got exception outside of a @test
  LoadError: IOError: could not spawn `java -version`: 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] #883
      @ ./process.jl:149 [inlined]
    [4] setup_stdios(f::Base.var"#883#884"{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] check_beast(; beast_jar::String)
      @ BeastUtils.RunBeast ~/.julia/packages/BeastUtils/o0ewH/src/RunBeast.jl:39
    [9] check_beast
      @ ~/.julia/packages/BeastUtils/o0ewH/src/RunBeast.jl:37 [inlined]
   [10] check_beast()
      @ PhylogeneticFactorAnalysis ~/.julia/packages/PhylogeneticFactorAnalysis/kZURZ/src/PhylogeneticFactorAnalysis.jl:62
   [11] top-level scope
      @ ~/.julia/packages/PhylogeneticFactorAnalysis/kZURZ/test/test.jl:5
   [12] include(mod::Module, _path::String)
      @ Base ./Base.jl:557
   [13] include(x::String)
      @ Main.var"##PFA test#230" ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:28
   [14] macro expansion
      @ ~/.julia/packages/PhylogeneticFactorAnalysis/kZURZ/test/runtests.jl:4 [inlined]
   [15] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined]
   [16] macro expansion
      @ ~/.julia/packages/PhylogeneticFactorAnalysis/kZURZ/test/runtests.jl:4 [inlined]
   [17] top-level scope
      @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:30
   [18] eval(m::Module, e::Any)
      @ Core ./boot.jl:430
   [19] macro expansion
      @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:28 [inlined]
   [20] macro expansion
      @ ./timing.jl:581 [inlined]
   [21] top-level scope
      @ ~/.julia/packages/PhylogeneticFactorAnalysis/kZURZ/test/runtests.jl:315
   [22] include(fname::String)
      @ Main ./sysimg.jl:38
   [23] top-level scope
      @ none:6
   [24] eval
      @ ./boot.jl:430 [inlined]
   [25] exec_options(opts::Base.JLOptions)
      @ Base ./client.jl:296
   [26] _start()
      @ Base ./client.jl:531
  in expression starting at /home/pkgeval/.julia/packages/PhylogeneticFactorAnalysis/kZURZ/test/test.jl:5
Test Summary: | Error  Total   Time
PFA test      |     1      1  11.1s
ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/PhylogeneticFactorAnalysis/kZURZ/test/runtests.jl:4

Testing failed after 47.69s

ERROR: LoadError: Package PhylogeneticFactorAnalysis 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 361.65s: package tests unexpectedly errored