Package evaluation to test PhylogeneticFactorAnalysis on Julia 1.12.7-DEV.42 (6f510b6086*) started at 2026-06-20T02:22:38.799 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 9.63s ################################################################################ # Installation # Installing PhylogeneticFactorAnalysis... Resolving package versions... Installed Crayons ───────────────────── v4.1.1 Installed libaec_jll ────────────────── v1.1.7+0 Installed Blosc_jll ─────────────────── v1.21.7+0 Installed MPICH_jll ─────────────────── v5.0.1+0 Installed IrrationalConstants ───────── v0.2.6 Installed MPIABI_jll ────────────────── v0.1.5+0 Installed MCMCDiagnostics ───────────── v0.4.0 Installed EzXML ─────────────────────── v1.2.3 Installed CSV ───────────────────────── v0.10.16 Installed aws_c_common_jll ──────────── v0.12.6+0 Installed XML2_jll ──────────────────── v2.13.9+0 Installed dlfcn_win32_jll ───────────── v1.4.2+0 Installed aws_c_auth_jll ────────────── v0.9.6+0 Installed Xorg_libpciaccess_jll ─────── v0.19.0+0 Installed Rmath ─────────────────────── v0.9.0 Installed HypergeometricFunctions ───── v0.3.28 Installed PrettyTables ──────────────── v3.3.2 Installed JSON ──────────────────────── v1.6.1 Installed aws_c_compression_jll ─────── v0.3.2+0 Installed TableTraits ───────────────── v1.0.1 Installed StatsFuns ─────────────────── v2.2.0 Installed H5Zblosc ──────────────────── v0.1.2 Installed Hwloc_jll ─────────────────── v2.14.0+0 Installed Zstd_jll ──────────────────── v1.5.7+1 Installed WinReg ────────────────────── v1.0.0 Installed Parsers ───────────────────── v2.8.6 Installed Conda ─────────────────────── v1.10.3 Installed SpecialFunctions ──────────── v2.8.0 Installed Preferences ───────────────── v1.5.2 Installed SentinelArrays ────────────── v1.4.10 Installed DataAPI ───────────────────── v1.16.0 Installed Tables ────────────────────── v1.12.1 Installed MicrosoftMPI_jll ──────────── v10.1.4+3 Installed PooledArrays ──────────────── v1.4.3 Installed CategoricalArrays ─────────── v0.10.7 Installed aws_c_http_jll ────────────── v0.10.13+0 Installed OpenMPI_jll ───────────────── v5.0.11+0 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed JLLWrappers ───────────────── v1.8.0 Installed InlineStrings ─────────────── v1.4.5 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed BeastUtils ────────────────── v1.0.0 Installed aws_c_io_jll ──────────────── v0.26.3+0 Installed RCall ─────────────────────── v0.13.18 Installed PrecompileTools ───────────── v1.3.4 Installed DataValueInterfaces ───────── v1.0.0 Installed PhylogeneticFactorAnalysis ── v1.0.0 Installed VersionParsing ────────────── v1.3.0 Installed WorkerUtilities ───────────── v1.6.1 Installed OrderedCollections ────────── v1.8.2 Installed JLD ───────────────────────── v0.13.5 Installed TranscodingStreams ────────── v0.11.3 Installed LaTeXStrings ──────────────── v1.4.0 Installed InvertedIndices ───────────── v1.3.1 Installed BEASTXMLConstructor ───────── v1.0.0 Installed Combinatorics ─────────────── v1.1.0 Installed DelimitedFiles ────────────── v1.9.1 Installed aws_checksums_jll ─────────── v0.2.10+0 Installed Reexport ──────────────────── v1.2.2 Installed FileIO ────────────────────── v1.19.0 Installed MPIPreferences ────────────── v0.1.12 Installed mpif_jll ──────────────────── v0.1.7+0 Installed FilePathsBase ─────────────── v0.9.24 Installed Rmath_jll ─────────────────── v0.5.1+0 Installed MPItrampoline_jll ─────────── v5.5.6+0 Installed Lz4_jll ───────────────────── v1.10.1+0 Installed Statistics ────────────────── v1.11.1 Installed StatsModels ───────────────── v0.7.10 Installed LogExpFunctions ───────────── v1.0.1 Installed DataFrames ────────────────── v1.8.2 Installed HDF5 ──────────────────────── v0.17.3 Installed WeakRefStrings ────────────── v1.4.3 Installed DataStructures ────────────── v0.18.22 Installed aws_c_sdkutils_jll ────────── v0.2.4+1 Installed ShiftedArrays ─────────────── v2.0.0 Installed StatsAPI ──────────────────── v1.8.0 Installed UnPack ────────────────────── v1.0.2 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed Compat ────────────────────── v4.18.1 Installed Requires ──────────────────── v1.3.1 Installed CodecZlib ─────────────────── v0.7.8 Installed LightXML ──────────────────── v0.9.3 Installed aws_c_cal_jll ─────────────── v0.9.13+0 Installed Missings ──────────────────── v1.2.0 Installed SortingAlgorithms ─────────── v1.2.2 Installed HDF5_jll ──────────────────── v2.1.2+0 Installed aws_c_s3_jll ──────────────── v0.11.5+0 Installed StatsBase ─────────────────── v0.33.10 Installed StructUtils ───────────────── v2.8.2 Installed s2n_tls_jll ───────────────── v1.7.3+0 Installed DocStringExtensions ───────── v0.9.5 Installed Blosc ─────────────────────── v0.7.3 Installed StringManipulation ────────── v0.4.4 Installing 24 artifacts Installed artifact aws_c_sdkutils 54.9 KiB Installed artifact aws_c_common 285.2 KiB Installed artifact aws_c_http 387.4 KiB Installed artifact Zstd 646.0 KiB Installed artifact Lz4 239.7 KiB Installed artifact Hwloc 3.5 MiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact XML2 2.5 MiB Installed artifact aws_c_s3 143.0 KiB Installed artifact s2n_tls 1.8 MiB Installed artifact Blosc 44.2 KiB Installed artifact aws_c_compression 13.4 KiB Installed artifact libaec 50.4 KiB Installed artifact Xorg_libpciaccess 26.2 KiB Installed artifact Rmath 121.9 KiB Installed artifact aws_checksums 87.0 KiB Installed artifact beast_jar 10.0 MiB Installed artifact testfiles 6.2 MiB Installed artifact aws_c_auth 130.3 KiB Installed artifact aws_c_io 181.7 KiB Installed artifact aws_c_cal 1.2 MiB Installed artifact Libiconv 1.9 MiB Installed artifact HDF5 6.1 MiB Installed artifact MPICH 8.8 MiB Updating `~/.julia/environments/v1.12/Project.toml` [88e69f3b] + PhylogeneticFactorAnalysis v1.0.0 Updating `~/.julia/environments/v1.12/Manifest.toml` [2ff12cca] + BEASTXMLConstructor v1.0.0 [af749cb1] + BeastUtils v1.0.0 [a74b3585] + Blosc v0.7.3 [336ed68f] + CSV v0.10.16 ⌅ [324d7699] + CategoricalArrays v0.10.7 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.1.0 [34da2185] + Compat v4.18.1 [8f4d0f93] + Conda v1.10.3 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.2 ⌅ [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 v1.19.0 [48062228] + FilePathsBase v0.9.24 [c8ec2601] + H5Zblosc v0.1.2 [f67ccb44] + HDF5 v0.17.3 [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 v1.8.0 [682c06a0] + JSON v1.6.1 [b964fa9f] + LaTeXStrings v1.4.0 [9c8b4983] + LightXML v0.9.3 [2ab3a3ac] + LogExpFunctions v1.0.1 [6e857e4b] + MCMCDiagnostics v0.4.0 [3da0fdf6] + MPIPreferences v0.1.12 [e1d29d7a] + Missings v1.2.0 ⌅ [bac558e1] + OrderedCollections v1.8.2 [69de0a69] + Parsers v2.8.6 [88e69f3b] + PhylogeneticFactorAnalysis v1.0.0 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [08abe8d2] + PrettyTables v3.3.2 ⌅ [6f49c342] + RCall v0.13.18 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [91c51154] + SentinelArrays v1.4.10 [1277b4bf] + ShiftedArrays v2.0.0 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.8.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 ⌅ [2913bbd2] + StatsBase v0.33.10 [4c63d2b9] + StatsFuns v2.2.0 [3eaba693] + StatsModels v0.7.10 [892a3eda] + StringManipulation v0.4.4 [ec057cc2] + StructUtils v2.8.2 [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 v1.4.3 [1b915085] + WinReg v1.0.0 [76eceee3] + WorkerUtilities v1.6.1 [0b7ba130] + Blosc_jll v1.21.7+0 [0234f1f7] + HDF5_jll v2.1.2+0 [e33a78d0] + Hwloc_jll v2.14.0+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [5ced341a] + Lz4_jll v1.10.1+0 [b5ada748] + MPIABI_jll v0.1.5+0 [7cb0a576] + MPICH_jll v5.0.1+0 [f1f71cc9] + MPItrampoline_jll v5.5.6+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [fe0851c0] + OpenMPI_jll v5.0.11+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 ⌅ [02c8fc9c] + XML2_jll v2.13.9+0 [a65dc6b1] + Xorg_libpciaccess_jll v0.19.0+0 [3161d3a3] + Zstd_jll v1.5.7+1 ⌅ [2b3700d1] + aws_c_auth_jll v0.9.6+0 [70f11efc] + aws_c_cal_jll v0.9.13+0 [73048d1d] + aws_c_common_jll v0.12.6+0 [73a04cd5] + aws_c_compression_jll v0.3.2+0 [3254fc65] + aws_c_http_jll v0.10.13+0 [13c41daa] + aws_c_io_jll v0.26.3+0 ⌅ [bd1f34fb] + aws_c_s3_jll v0.11.5+0 [1282aa60] + aws_c_sdkutils_jll v0.2.4+1 [b2a88e68] + aws_checksums_jll v0.2.10+0 [c4b69c83] + dlfcn_win32_jll v1.4.2+0 [477f73a3] + libaec_jll v1.1.7+0 [9aeb927a] + mpif_jll v0.1.7+0 [cddc5d3d] + s2n_tls_jll v1.7.3+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [f43a241f] + Downloads v1.7.0 [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 v0.6.4 [76f85450] + LibGit2 v1.11.0 [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 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.12.1 [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 v1.12.0 [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 v1.3.0+1 [deac9b47] + LibCURL_jll v8.15.0+0 [e37daf67] + LibGit2_jll v1.9.0+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 v3.5.6+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.64.0+1 [3f19e933] + p7zip_jll v17.7.0+0 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/8f06b0cfa4c514c7b9546756dbae91fcfbc92dc9/build.log` Building RCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/3084689b18f9e5e817a6ce9a83a7654d8ad0f2f6/build.log` Installation completed after 123.84s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4266.3 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 26 already precompiled. 24 dependencies precompiled but different versions are currently loaded (ArgTools, Base64, Dates, Downloads, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, Logging, Markdown, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, Pkg, Printf, StyledStrings, TOML, Tar, UUIDs, Zlib_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 1 dependent of these packages may trigger further precompilation to work with the unexpected versions. Precompiling package dependencies... Precompiling packages... 2382.1 ms ✓ Combinatorics 4102.9 ms ✓ OrderedCollections 785.5 ms ✓ UnPack 738.0 ms ✓ DataValueInterfaces 825.3 ms ✓ LaTeXStrings 857.0 ms ✓ InvertedIndices 784.2 ms ✓ Reexport 1139.2 ms ✓ DocStringExtensions 1773.7 ms ✓ InlineStrings 1123.4 ms ✓ Statistics 5116.2 ms ✓ IrrationalConstants 760.7 ms ✓ IteratorInterfaceExtensions 866.0 ms ✓ DataAPI 1187.7 ms ✓ WorkerUtilities 866.8 ms ✓ StatsAPI 4814.5 ms ✓ Crayons 712.6 ms ✓ SafeTestsets 1105.1 ms ✓ VersionParsing 1276.8 ms ✓ TranscodingStreams 1095.4 ms ✓ WinReg 836.1 ms ✓ ShiftedArrays 936.4 ms ✓ DelimitedFiles 1168.9 ms ✓ Requires 3088.7 ms ✓ SentinelArrays 4287.1 ms ✓ StructUtils 4097.0 ms ✓ Compat 1170.1 ms ✓ Preferences 1385.5 ms ✓ Statistics → SparseArraysExt 1349.6 ms ✓ LogExpFunctions 738.6 ms ✓ TableTraits 3672.6 ms ✓ Missings 1009.4 ms ✓ PooledArrays 937.6 ms ✓ CodecZlib 9049.3 ms ✓ FileIO 846.7 ms ✓ Compat → CompatLinearAlgebraExt 1453.2 ms ✓ MPIPreferences 1025.1 ms ✓ PrecompileTools 1770.6 ms ✓ JLLWrappers 4894.7 ms ✓ Tables 7577.7 ms ✓ CategoricalArrays 3915.3 ms ✓ DataStructures 2320.3 ms ✓ FilePathsBase 3371.1 ms ✓ StringManipulation 14479.9 ms ✓ Parsers 1370.2 ms ✓ Rmath_jll 1095.3 ms ✓ MicrosoftMPI_jll 1028.0 ms ✓ dlfcn_win32_jll 1374.5 ms ✓ Zstd_jll 1460.4 ms ✓ aws_c_common_jll 1455.5 ms ✓ Libiconv_jll 1446.2 ms ✓ Lz4_jll 4231.2 ms ✓ MPItrampoline_jll 1305.3 ms ✓ Xorg_libpciaccess_jll 1384.8 ms ✓ OpenSpecFun_jll 1406.5 ms ✓ libaec_jll 1455.0 ms ✓ s2n_tls_jll 876.1 ms ✓ StructUtils → StructUtilsTablesExt 1623.9 ms ✓ SortingAlgorithms 3378.1 ms ✓ FilePathsBase → FilePathsBaseTestExt 1361.7 ms ✓ FilePathsBase → FilePathsBaseMmapExt 51122.3 ms ✓ PrettyTables 11126.8 ms ✓ JSON 1515.5 ms ✓ InlineStrings → ParsersExt 1606.3 ms ✓ Rmath 1422.7 ms ✓ aws_checksums_jll 1441.8 ms ✓ aws_c_cal_jll 1402.1 ms ✓ aws_c_sdkutils_jll 1383.5 ms ✓ aws_c_compression_jll 1434.5 ms ✓ XML2_jll 1444.4 ms ✓ Blosc_jll 5812.7 ms ✓ SpecialFunctions 11909.6 ms ✓ StatsBase 88715.2 ms ✓ DataFrames 1903.3 ms ✓ Conda 2266.5 ms ✓ WeakRefStrings 1409.5 ms ✓ aws_c_io_jll 1034.8 ms ✓ LightXML 1778.3 ms ✓ EzXML 1431.3 ms ✓ Hwloc_jll 1112.3 ms ✓ Blosc 2296.3 ms ✓ HypergeometricFunctions 4707.9 ms ✓ MCMCDiagnostics 31354.0 ms ✓ CSV 1388.8 ms ✓ aws_c_http_jll 4330.1 ms ✓ MPIABI_jll 4311.0 ms ✓ OpenMPI_jll 1504.2 ms ✓ MPICH_jll 5082.1 ms ✓ StatsFuns 13925.8 ms ✓ BEASTXMLConstructor 1401.7 ms ✓ aws_c_auth_jll 4299.7 ms ✓ mpif_jll 9311.5 ms ✓ StatsModels 1398.6 ms ✓ aws_c_s3_jll 19520.8 ms ✓ RCall 1721.1 ms ✓ HDF5_jll 14209.2 ms ✓ HDF5 1815.4 ms ✓ H5Zblosc 8088.8 ms ✓ JLD 20034.8 ms ✓ BeastUtils 32866.3 ms ✓ PhylogeneticFactorAnalysis 100 dependencies successfully precompiled in 509 seconds. 37 already precompiled. 24 dependencies precompiled but different versions are currently loaded (ArgTools, Base64, Dates, Downloads, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, Logging, Markdown, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, Pkg, Printf, StyledStrings, TOML, Tar, UUIDs, Zlib_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 77 dependents of these packages may trigger further precompilation to work with the unexpected versions. 3 dependencies had output during precompilation: ┌ 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. └ ┌ 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 └ ┌ 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 531.87s ################################################################################ # Testing # Testing PhylogeneticFactorAnalysis Status `/tmp/jl_yGXOnq/Project.toml` [2ff12cca] BEASTXMLConstructor v1.0.0 [af749cb1] BeastUtils v1.0.0 [336ed68f] CSV v0.10.16 [861a8166] Combinatorics v1.1.0 [a93c6f00] DataFrames v1.8.2 [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 v1.12.0 [44cfe95a] Pkg v1.12.1 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_yGXOnq/Manifest.toml` [2ff12cca] BEASTXMLConstructor v1.0.0 [af749cb1] BeastUtils v1.0.0 [a74b3585] Blosc v0.7.3 [336ed68f] CSV v0.10.16 ⌅ [324d7699] CategoricalArrays v0.10.7 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.1.0 [34da2185] Compat v4.18.1 [8f4d0f93] Conda v1.10.3 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.2 ⌅ [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 v1.19.0 [48062228] FilePathsBase v0.9.24 [c8ec2601] H5Zblosc v0.1.2 [f67ccb44] HDF5 v0.17.3 [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 v1.8.0 [682c06a0] JSON v1.6.1 [b964fa9f] LaTeXStrings v1.4.0 [9c8b4983] LightXML v0.9.3 [2ab3a3ac] LogExpFunctions v1.0.1 [6e857e4b] MCMCDiagnostics v0.4.0 [3da0fdf6] MPIPreferences v0.1.12 [e1d29d7a] Missings v1.2.0 ⌅ [bac558e1] OrderedCollections v1.8.2 [69de0a69] Parsers v2.8.6 [88e69f3b] PhylogeneticFactorAnalysis v1.0.0 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [08abe8d2] PrettyTables v3.3.2 ⌅ [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 v1.4.10 [1277b4bf] ShiftedArrays v2.0.0 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.8.0 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 ⌅ [2913bbd2] StatsBase v0.33.10 [4c63d2b9] StatsFuns v2.2.0 [3eaba693] StatsModels v0.7.10 [892a3eda] StringManipulation v0.4.4 [ec057cc2] StructUtils v2.8.2 [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 v1.4.3 [1b915085] WinReg v1.0.0 [76eceee3] WorkerUtilities v1.6.1 [0b7ba130] Blosc_jll v1.21.7+0 [0234f1f7] HDF5_jll v2.1.2+0 [e33a78d0] Hwloc_jll v2.14.0+0 [94ce4f54] Libiconv_jll v1.18.0+0 [5ced341a] Lz4_jll v1.10.1+0 [b5ada748] MPIABI_jll v0.1.5+0 [7cb0a576] MPICH_jll v5.0.1+0 [f1f71cc9] MPItrampoline_jll 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LazyArtifacts v1.11.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [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 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.12.1 [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 v1.12.0 [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 v1.3.0+1 [deac9b47] LibCURL_jll v8.15.0+0 [e37daf67] LibGit2_jll v1.9.0+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 v3.5.6+0 [bea87d4a] SuiteSparse_jll v7.8.3+2 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.64.0+1 [3f19e933] p7zip_jll v17.7.0+0 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:139 [2] _spawn @ ./process.jl:156 [inlined] [3] #_spawn##0 @ ./process.jl:148 [inlined] [4] setup_stdios(f::Base.var"#_spawn##0#_spawn##1"{Cmd}, stdios::Vector{Union{RawFD, Base.FileRedirect, IO}}) @ Base ./process.jl:235 [5] _spawn @ ./process.jl:147 [inlined] [6] run(::Cmd; wait::Bool) @ Base ./process.jl:511 [7] run @ ./process.jl:509 [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:307 [13] top-level scope @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:30 [14] macro expansion @ ~/.julia/packages/PhylogeneticFactorAnalysis/kZURZ/test/runtests.jl:4 [inlined] [15] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1777 [inlined] [16] macro expansion @ ~/.julia/packages/PhylogeneticFactorAnalysis/kZURZ/test/runtests.jl:4 [inlined] [17] eval(m::Module, e::Any) @ Core ./boot.jl:489 [18] macro expansion @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:28 [inlined] [19] macro expansion @ ./timing.jl:697 [inlined] [20] top-level scope @ ~/.julia/packages/PhylogeneticFactorAnalysis/kZURZ/test/runtests.jl:353 [21] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:307 [22] top-level scope @ none:6 [23] eval(m::Module, e::Any) @ Core ./boot.jl:489 [24] exec_options(opts::Base.JLOptions) @ Base ./client.jl:283 [25] _start() @ Base ./client.jl:550 in expression starting at /home/pkgeval/.julia/packages/PhylogeneticFactorAnalysis/kZURZ/test/test.jl:5 Test Summary: | Error Total Time PFA test | 1 1 7.4s RNG of the outermost testset: Random.Xoshiro(0x8aacc470d0b180bf, 0xa81df8ba2d8f510c, 0x101c7b9ce1261995, 0x8fd62fcecd4cd2ce, 0xc27067575c37b76e) 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 73.75s ERROR: LoadError: Package PhylogeneticFactorAnalysis 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:2538 [3] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2387 [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:552 [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:169 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 [7] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:156 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:306 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:317 [12] _start() @ Base ./client.jl:550 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 774.07s: package tests unexpectedly errored