Package evaluation to test PhylogeneticFactorAnalysis on Julia 1.14.0-DEV.1299 (6d6224db99*) started at 2025-11-27T20:04:17.630 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.13s ################################################################################ # Installation # Installing PhylogeneticFactorAnalysis... Resolving package versions... Installed Rmath_jll ─────────────────── v0.5.1+0 Installed Lz4_jll ───────────────────── v1.10.1+0 Installed VersionParsing ────────────── v1.3.0 Installed LightXML ──────────────────── v0.9.3 Installed FilePathsBase ─────────────── v0.9.24 Installed InlineStrings ─────────────── v1.4.5 Installed RCall ─────────────────────── v0.13.18 Installed DataStructures ────────────── v0.18.22 Installed libaec_jll ────────────────── v1.1.4+0 Installed HypergeometricFunctions ───── v0.3.28 Installed StatsModels ───────────────── v0.7.7 Installed DelimitedFiles ────────────── v1.9.1 Installed MPICH_jll ─────────────────── v4.3.2+0 Installed CodecZlib ─────────────────── v0.7.8 Installed StatsBase ─────────────────── v0.33.21 Installed MicrosoftMPI_jll ──────────── v10.1.4+3 Installed Compat ────────────────────── v4.18.1 Installed OrderedCollections ────────── v1.8.1 Installed ShiftedArrays ─────────────── v2.0.0 Installed Combinatorics ─────────────── v1.0.3 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed TranscodingStreams ────────── v0.11.3 Installed DataAPI ───────────────────── v1.16.0 Installed StatsAPI ──────────────────── v1.7.1 Installed InvertedIndices ───────────── v1.3.1 Installed Blosc ─────────────────────── v0.7.3 Installed Statistics ────────────────── v1.11.1 Installed DataValueInterfaces ───────── v1.0.0 Installed PrecompileTools ───────────── v1.3.3 Installed SentinelArrays ────────────── v1.4.8 Installed Conda ─────────────────────── v1.10.3 Installed JLD ───────────────────────── v0.13.5 Installed Blosc_jll ─────────────────── v1.21.7+0 Installed WinReg ────────────────────── v1.0.0 Installed StructUtils ───────────────── v2.6.0 Installed FileIO ────────────────────── v1.17.1 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed IrrationalConstants ───────── v0.2.6 Installed Requires ──────────────────── v1.3.1 Installed StringManipulation ────────── v0.4.2 Installed HDF5_jll ──────────────────── v1.14.6+0 Installed OpenMPI_jll ───────────────── v5.0.9+0 Installed LogExpFunctions ───────────── v0.3.29 Installed Parsers ───────────────────── v2.8.3 Installed JSON ──────────────────────── v1.3.0 Installed BEASTXMLConstructor ───────── v1.0.0 Installed Hwloc_jll ─────────────────── v2.12.1+0 Installed PrettyTables ──────────────── v3.1.2 Installed Rmath ─────────────────────── v0.9.0 Installed Tables ────────────────────── v1.12.1 Installed StatsFuns ─────────────────── v1.5.2 Installed XML2_jll ──────────────────── v2.15.1+0 Installed CSV ───────────────────────── v0.10.15 Installed H5Zblosc ──────────────────── v0.1.2 Installed SpecialFunctions ──────────── v2.6.1 Installed Reexport ──────────────────── v1.2.2 Installed PhylogeneticFactorAnalysis ── v1.0.0 Installed Preferences ───────────────── v1.5.0 Installed DataFrames ────────────────── v1.8.1 Installed Missings ──────────────────── v1.2.0 Installed MPIPreferences ────────────── v0.1.11 Installed WeakRefStrings ────────────── v1.4.2 Installed EzXML ─────────────────────── v1.2.3 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed PooledArrays ──────────────── v1.4.3 Installed JLLWrappers ───────────────── v1.7.1 Installed TableTraits ───────────────── v1.0.1 Installed LaTeXStrings ──────────────── v1.4.0 Installed MPItrampoline_jll ─────────── v5.5.4+0 Installed Crayons ───────────────────── v4.1.1 Installed SortingAlgorithms ─────────── v1.2.2 Installed CategoricalArrays ─────────── v0.10.7 Installed HDF5 ──────────────────────── v0.17.2 Installed MCMCDiagnostics ───────────── v0.4.0 Installed UnPack ────────────────────── v1.0.2 Installed WorkerUtilities ───────────── v1.6.1 Installed BeastUtils ────────────────── v1.0.0 Installed DocStringExtensions ───────── v0.9.5 Installing 11 artifacts Installed artifact Rmath 121.9 KiB Installed artifact libaec 49.6 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact Blosc 44.2 KiB Installed artifact Lz4 239.7 KiB Installed artifact XML2 2.2 MiB Installed artifact Hwloc 3.5 MiB Installed artifact Libiconv 1.9 MiB Installed artifact HDF5 5.7 MiB Installed artifact MPICH 3.3 MiB Installed artifact beast_jar 10.0 MiB Updating `~/.julia/environments/v1.14/Project.toml` [88e69f3b] + PhylogeneticFactorAnalysis v1.0.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [2ff12cca] + BEASTXMLConstructor v1.0.0 [af749cb1] + BeastUtils v1.0.0 [a74b3585] + Blosc v0.7.3 [336ed68f] + CSV v0.10.15 ⌅ [324d7699] + CategoricalArrays v0.10.7 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.0.3 [34da2185] + Compat v4.18.1 [8f4d0f93] + Conda v1.10.3 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 ⌅ [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [ffbed154] + DocStringExtensions v0.9.5 [8f5d6c58] + EzXML v1.2.3 [5789e2e9] + FileIO v1.17.1 [48062228] + FilePathsBase v0.9.24 [c8ec2601] + H5Zblosc v0.1.2 [f67ccb44] + HDF5 v0.17.2 [34004b35] + HypergeometricFunctions v0.3.28 [842dd82b] + InlineStrings v1.4.5 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [4138dd39] + JLD v0.13.5 [692b3bcd] + JLLWrappers v1.7.1 [682c06a0] + JSON v1.3.0 [b964fa9f] + LaTeXStrings v1.4.0 [9c8b4983] + LightXML v0.9.3 [2ab3a3ac] + LogExpFunctions v0.3.29 [6e857e4b] + MCMCDiagnostics v0.4.0 [3da0fdf6] + MPIPreferences v0.1.11 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.3 [88e69f3b] + PhylogeneticFactorAnalysis v1.0.0 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [08abe8d2] + PrettyTables v3.1.2 ⌅ [6f49c342] + RCall v0.13.18 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [91c51154] + SentinelArrays v1.4.8 [1277b4bf] + ShiftedArrays v2.0.0 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 ⌅ [2913bbd2] + StatsBase v0.33.21 [4c63d2b9] + StatsFuns v1.5.2 [3eaba693] + StatsModels v0.7.7 [892a3eda] + StringManipulation v0.4.2 [ec057cc2] + StructUtils v2.6.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [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 v2.12.1+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [5ced341a] + Lz4_jll v1.10.1+0 [7cb0a576] + MPICH_jll v4.3.2+0 [f1f71cc9] + MPItrampoline_jll v5.5.4+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [fe0851c0] + OpenMPI_jll v5.0.9+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [02c8fc9c] + XML2_jll v2.15.1+0 [477f73a3] + libaec_jll v1.1.4+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.13.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.17.0+0 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.11.4 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Building Conda → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/8f06b0cfa4c514c7b9546756dbae91fcfbc92dc9/build.log` Building RCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/3084689b18f9e5e817a6ce9a83a7654d8ad0f2f6/build.log` Installation completed after 149.76s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. 4437.6 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. 1 dependency had output during precompilation: ┌ TestEnv │ WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. └ ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ UndefVarError: `project_rel_path` not defined in `TestEnv` │ Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value. │ Stacktrace: │ [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:9 │ [6] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:24 │ [7] include(mod::Module, _path::String) │ @ Base ./Base.jl:309 │ [8] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:344 │ [9] _start() │ @ Base ./client.jl:577 └ @ Main /PkgEval.jl/scripts/precompile.jl:26 Precompiling package dependencies... Precompiling packages... 1763.6 ms ✓ InlineStrings 746.6 ms ✓ Reexport 1085.3 ms ✓ Statistics 852.1 ms ✓ DataAPI 1957.2 ms ✓ IrrationalConstants 809.8 ms ✓ UnPack 768.2 ms ✓ DataValueInterfaces 823.0 ms ✓ StatsAPI 1104.9 ms ✓ Requires 1190.4 ms ✓ OrderedCollections 875.2 ms ✓ InvertedIndices 1122.7 ms ✓ DocStringExtensions 876.0 ms ✓ ShiftedArrays 920.1 ms ✓ VersionParsing 849.1 ms ✓ WinReg 2058.6 ms ✓ Combinatorics 1039.2 ms ✓ WorkerUtilities 1334.2 ms ✓ TranscodingStreams 752.9 ms ✓ IteratorInterfaceExtensions 839.1 ms ✓ LaTeXStrings 1845.3 ms ✓ Crayons 982.7 ms ✓ DelimitedFiles 2804.0 ms ✓ SentinelArrays 1356.4 ms ✓ StructUtils 1150.1 ms ✓ Compat 1080.6 ms ✓ Preferences 1257.7 ms ✓ Statistics → SparseArraysExt 934.4 ms ✓ Missings 980.0 ms ✓ PooledArrays 9127.2 ms ✓ FileIO 1393.9 ms ✓ LogExpFunctions 975.4 ms ✓ CodecZlib 774.1 ms ✓ TableTraits 850.4 ms ✓ Compat → CompatLinearAlgebraExt 1243.1 ms ✓ JLLWrappers 1383.0 ms ✓ MPIPreferences 910.9 ms ✓ PrecompileTools 6902.4 ms ✓ CategoricalArrays 1716.4 ms ✓ Tables 1970.3 ms ✓ FilePathsBase 3612.3 ms ✓ DataStructures 1354.2 ms ✓ libaec_jll 1488.9 ms ✓ Libiconv_jll 1471.1 ms ✓ Lz4_jll 1440.0 ms ✓ Hwloc_jll 1427.4 ms ✓ Rmath_jll 1175.8 ms ✓ MicrosoftMPI_jll 1465.5 ms ✓ OpenSpecFun_jll 4864.9 ms ✓ MPItrampoline_jll 3207.1 ms ✓ StringManipulation 16660.6 ms ✓ Parsers 879.9 ms ✓ StructUtils → StructUtilsTablesExt 883.2 ms ✓ FilePathsBase → FilePathsBaseMmapExt 1535.4 ms ✓ SortingAlgorithms 1441.4 ms ✓ XML2_jll 1421.8 ms ✓ Blosc_jll 5097.0 ms ✓ MPICH_jll 4622.4 ms ✓ OpenMPI_jll 1496.5 ms ✓ Rmath 4835.6 ms ✓ SpecialFunctions 36613.3 ms ✓ PrettyTables 6840.6 ms ✓ JSON 976.5 ms ✓ InlineStrings → ParsersExt 8775.9 ms ✓ StatsBase 1056.4 ms ✓ LightXML 1831.4 ms ✓ EzXML 1123.0 ms ✓ Blosc 5702.2 ms ✓ HDF5_jll 2451.8 ms ✓ HypergeometricFunctions 90862.7 ms ✓ DataFrames 2477.6 ms ✓ Conda 2564.1 ms ✓ WeakRefStrings 3020.5 ms ✓ MCMCDiagnostics 15112.1 ms ✓ HDF5 2777.2 ms ✓ StatsFuns 28659.6 ms ✓ CSV 5910.8 ms ✓ H5Zblosc 9630.6 ms ✓ StatsModels WARNING: method definition for #add_parameter#23 at /home/pkgeval/.julia/packages/BEASTXMLConstructor/OclAi/src/XMLConstructor/XMLElements/MatrixParameter.jl:78 declares type variable T but does not use it. 17485.4 ms ✓ BEASTXMLConstructor 8024.1 ms ✓ JLD 14997.7 ms ✓ RCall ┌ 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 22169.5 ms ✓ BeastUtils ┌ 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 28155.6 ms ✓ PhylogeneticFactorAnalysis 83 dependencies successfully precompiled in 439 seconds. 37 already precompiled. 3 dependencies had output during precompilation: ┌ PhylogeneticFactorAnalysis │ ┌ 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 └ ┌ BEASTXMLConstructor │ WARNING: method definition for #add_parameter#23 at /home/pkgeval/.julia/packages/BEASTXMLConstructor/OclAi/src/XMLConstructor/XMLElements/MatrixParameter.jl:78 declares type variable T but does not use it. └ ┌ BeastUtils │ ┌ 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 └ Precompilation completed after 458.36s ################################################################################ # Testing # Testing PhylogeneticFactorAnalysis Status `/tmp/jl_ugQKtr/Project.toml` [2ff12cca] BEASTXMLConstructor v1.0.0 [af749cb1] BeastUtils v1.0.0 [336ed68f] CSV v0.10.15 [861a8166] Combinatorics v1.0.3 [a93c6f00] DataFrames v1.8.1 [8f5d6c58] EzXML v1.2.3 [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 v1.13.0 [44cfe95a] Pkg v1.13.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_ugQKtr/Manifest.toml` [2ff12cca] BEASTXMLConstructor v1.0.0 [af749cb1] BeastUtils v1.0.0 [a74b3585] Blosc v0.7.3 [336ed68f] CSV v0.10.15 ⌅ [324d7699] CategoricalArrays v0.10.7 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.0.3 [34da2185] Compat v4.18.1 [8f4d0f93] Conda v1.10.3 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [ffbed154] DocStringExtensions v0.9.5 [8f5d6c58] EzXML v1.2.3 [5789e2e9] FileIO v1.17.1 [48062228] FilePathsBase v0.9.24 [c8ec2601] H5Zblosc v0.1.2 [f67ccb44] HDF5 v0.17.2 [34004b35] HypergeometricFunctions v0.3.28 [842dd82b] InlineStrings v1.4.5 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [4138dd39] JLD v0.13.5 [692b3bcd] JLLWrappers v1.7.1 [682c06a0] JSON v1.3.0 [b964fa9f] LaTeXStrings v1.4.0 [9c8b4983] LightXML v0.9.3 [2ab3a3ac] LogExpFunctions v0.3.29 [6e857e4b] MCMCDiagnostics v0.4.0 [3da0fdf6] MPIPreferences v0.1.11 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.1 [69de0a69] Parsers v2.8.3 [88e69f3b] PhylogeneticFactorAnalysis v1.0.0 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.1.2 ⌅ [6f49c342] RCall v0.13.18 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [1bc83da4] SafeTestsets v0.1.0 [91c51154] SentinelArrays v1.4.8 [1277b4bf] ShiftedArrays v2.0.0 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 ⌅ [2913bbd2] StatsBase v0.33.21 [4c63d2b9] StatsFuns v1.5.2 [3eaba693] StatsModels v0.7.7 [892a3eda] StringManipulation v0.4.2 [ec057cc2] StructUtils v2.6.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [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 v2.12.1+0 [94ce4f54] Libiconv_jll v1.18.0+0 [5ced341a] Lz4_jll v1.10.1+0 [7cb0a576] MPICH_jll v4.3.2+0 [f1f71cc9] MPItrampoline_jll v5.5.4+0 [9237b28f] MicrosoftMPI_jll v10.1.4+3 [fe0851c0] OpenMPI_jll v5.0.9+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [02c8fc9c] XML2_jll v2.15.1+0 [477f73a3] libaec_jll v1.1.4+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v1.0.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.13.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [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 v1.3.0+1 [deac9b47] LibCURL_jll v8.17.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints 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.IOServer, Base.SyncCloseFD, IO}}) @ Base ./process.jl:149 [2] _spawn @ ./process.jl:166 [inlined] [3] #_spawn##0 @ ./process.jl:158 [inlined] [4] setup_stdios(f::Base.var"#_spawn##0#_spawn##1"{Cmd}, stdios::Vector{Union{RawFD, Base.FileRedirect, Base.IOServer, IO}}) @ Base ./process.jl:245 [5] _spawn @ ./process.jl:157 [inlined] [6] run(::Cmd; wait::Bool) @ Base ./process.jl:525 [7] run @ ./process.jl:523 [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(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [13] top-level scope @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:4 [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [15] macro expansion @ ~/.julia/packages/PhylogeneticFactorAnalysis/kZURZ/test/runtests.jl:4 [inlined] [16] eval(m::Module, e::Any) @ Core ./boot.jl:489 [17] macro expansion @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:28 [inlined] [18] macro expansion @ ./timing.jl:730 [inlined] [19] top-level scope @ ~/.julia/packages/PhylogeneticFactorAnalysis/kZURZ/test/runtests.jl:394 [20] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [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:310 [24] _start() @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/PhylogeneticFactorAnalysis/kZURZ/test/test.jl:5 Test Summary: | Error Total Time PFA test | 1 1 11.3s RNG of the outermost testset: Random.Xoshiro(0xafc9826a47a2d9e5, 0x5d6d18059aa74de6, 0x221de3a8fa3e8803, 0xa53ee4429dde8162, 0xf75e7a9a4be6f554) 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 82.85s ERROR: LoadError: Package PhylogeneticFactorAnalysis errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/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/v1.14/Pkg/src/Operations.jl:2946 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2795 [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/v1.14/Pkg/src/API.jl:572 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:548 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 738.1s: package tests unexpectedly errored