Package evaluation to test RedClust on Julia 1.14.0-DEV.1372 (893635dc59*) started at 2025-12-16T19:43:59.351 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 10.01s ################################################################################ # Installation # Installing RedClust... Resolving package versions... Installed Rmath_jll ──────────────────────── v0.5.1+0 Installed CommonWorldInvalidations ───────── v1.0.0 Installed Adapt ──────────────────────────── v4.4.0 Installed ManualMemory ───────────────────── v0.1.8 Installed AbstractTrees ──────────────────── v0.4.5 Installed FillArrays ─────────────────────── v1.15.0 Installed VectorizationBase ──────────────── v0.21.72 Installed libaec_jll ─────────────────────── v1.1.4+0 Installed MPICH_jll ──────────────────────── v4.3.2+0 Installed DataStructures ─────────────────── v0.19.3 Installed HypergeometricFunctions ────────── v0.3.28 Installed BitTwiddlingConvenienceFunctions ─ v0.1.6 Installed SLEEFPirates ───────────────────── v0.6.43 Installed AliasTables ────────────────────── v1.1.3 Installed StatsBase ──────────────────────── v0.34.9 Installed MicrosoftMPI_jll ───────────────── v10.1.4+3 Installed SIMDTypes ──────────────────────── v0.1.0 Installed OrderedCollections ─────────────── v1.8.1 Installed Compat ─────────────────────────── v4.18.1 Installed ArrayInterface ─────────────────── v7.22.0 Installed HostCPUFeatures ────────────────── v0.1.18 Installed NearestNeighbors ───────────────── v0.4.26 Installed DataAPI ────────────────────────── v1.16.0 Installed LoopVectorization ──────────────── v0.12.173 Installed Statistics ─────────────────────── v1.11.1 Installed Xorg_libpciaccess_jll ──────────── v0.18.1+0 Installed StatsAPI ───────────────────────── v1.8.0 Installed PrecompileTools ────────────────── v1.3.3 Installed CpuId ──────────────────────────── v0.3.1 Installed StaticArraysCore ───────────────── v1.4.4 Installed LayoutPointers ─────────────────── v0.1.17 Installed OffsetArrays ───────────────────── v1.17.0 Installed IrrationalConstants ────────────── v0.2.6 Installed StaticArrays ───────────────────── v1.9.15 Installed Clustering ─────────────────────── v0.15.8 Installed Distances ──────────────────────── v0.10.12 Installed RedClust ───────────────────────── v1.2.2 Installed StaticArrayInterface ───────────── v1.8.0 Installed SciMLPublic ────────────────────── v1.0.0 Installed CPUSummary ─────────────────────── v0.2.7 Installed OpenSpecFun_jll ────────────────── v0.5.6+0 Installed QuadGK ─────────────────────────── v2.11.2 Installed HDF5_jll ───────────────────────── v1.14.6+0 Installed Requires ───────────────────────── v1.3.1 Installed LogExpFunctions ────────────────── v0.3.29 Installed OpenMPI_jll ────────────────────── v5.0.9+0 Installed Hwloc_jll ──────────────────────── v2.12.2+0 Installed IfElse ─────────────────────────── v0.1.1 Installed Rmath ──────────────────────────── v0.9.0 Installed PtrArrays ──────────────────────── v1.3.0 Installed CloseOpenIntervals ─────────────── v0.1.13 Installed StatsFuns ──────────────────────── v1.5.2 Installed XML2_jll ───────────────────────── v2.13.9+0 Installed Missings ───────────────────────── v1.2.0 Installed Reexport ───────────────────────── v1.2.2 Installed SpecialFunctions ───────────────── v2.6.1 Installed Static ─────────────────────────── v1.3.1 Installed Preferences ────────────────────── v1.5.0 Installed MPIPreferences ─────────────────── v0.1.11 Installed Distributions ──────────────────── v0.25.122 Installed Libiconv_jll ───────────────────── v1.18.0+0 Installed JLLWrappers ────────────────────── v1.7.1 Installed PDMats ─────────────────────────── v0.11.36 Installed ProgressBars ───────────────────── v1.5.1 Installed MPItrampoline_jll ──────────────── v5.5.4+0 Installed ThreadingUtilities ─────────────── v0.5.5 Installed PolyesterWeave ─────────────────── v0.2.2 Installed SortingAlgorithms ──────────────── v1.2.2 Installed UnPack ─────────────────────────── v1.0.2 Installed DocStringExtensions ────────────── v0.9.5 Installed HDF5 ───────────────────────────── v0.17.2 Installing 9 artifacts Installed artifact Xorg_libpciaccess 24.8 KiB Installed artifact libaec 49.6 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact Rmath 121.9 KiB Installed artifact Libiconv 1.9 MiB Installed artifact Hwloc 3.5 MiB Installed artifact MPICH 3.3 MiB Installed artifact XML2 2.5 MiB Installed artifact HDF5 5.7 MiB Updating `~/.julia/environments/v1.14/Project.toml` [bf1adee6] + RedClust v1.2.2 Updating `~/.julia/environments/v1.14/Manifest.toml` [1520ce14] + AbstractTrees v0.4.5 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.22.0 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [2a0fbf3d] + CPUSummary v0.2.7 [fb6a15b2] + CloseOpenIntervals v0.1.13 [aaaa29a8] + Clustering v0.15.8 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [adafc99b] + CpuId v0.3.1 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.3 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.15.0 [f67ccb44] + HDF5 v0.17.2 [3e5b6fbb] + HostCPUFeatures v0.1.18 [34004b35] + HypergeometricFunctions v0.3.28 [615f187c] + IfElse v0.1.1 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.7.1 [10f19ff3] + LayoutPointers v0.1.17 [2ab3a3ac] + LogExpFunctions v0.3.29 [bdcacae8] + LoopVectorization v0.12.173 [3da0fdf6] + MPIPreferences v0.1.11 [d125e4d3] + ManualMemory v0.1.8 [e1d29d7a] + Missings v1.2.0 [b8a86587] + NearestNeighbors v0.4.26 [6fe1bfb0] + OffsetArrays v1.17.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.36 [1d0040c9] + PolyesterWeave v0.2.2 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [49802e3a] + ProgressBars v1.5.1 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [bf1adee6] + RedClust v1.2.2 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.43 [431bcebd] + SciMLPublic v1.0.0 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [aedffcd0] + Static v1.3.1 [0d7ed370] + StaticArrayInterface v1.8.0 [90137ffa] + StaticArrays v1.9.15 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.9 [4c63d2b9] + StatsFuns v1.5.2 [8290d209] + ThreadingUtilities v0.5.5 [3a884ed6] + UnPack v1.0.2 [3d5dd08c] + VectorizationBase v0.21.72 ⌅ [0234f1f7] + HDF5_jll v1.14.6+0 [e33a78d0] + Hwloc_jll v2.12.2+0 [94ce4f54] + Libiconv_jll v1.18.0+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 v2.13.9+0 [a65dc6b1] + Xorg_libpciaccess_jll v0.18.1+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 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [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 v1.14.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [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 v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.12.2 [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 ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 14.15s ################################################################################ # Precompilation # ERROR: LoadError: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Nothing) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:10 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/precompile.jl:6 caused by: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Base.DevNull) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:7 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:577 Precompilation failed after 11.17s ################################################################################ # Testing # Testing RedClust Status `/tmp/jl_Q1J2Eq/Project.toml` [aaaa29a8] Clustering v0.15.8 [bf1adee6] RedClust v1.2.2 [2913bbd2] StatsBase v0.34.9 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_Q1J2Eq/Manifest.toml` [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.22.0 [62783981] BitTwiddlingConvenienceFunctions v0.1.6 [2a0fbf3d] CPUSummary v0.2.7 [fb6a15b2] CloseOpenIntervals v0.1.13 [aaaa29a8] Clustering v0.15.8 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.18.1 [adafc99b] CpuId v0.3.1 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.19.3 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [1a297f60] FillArrays v1.15.0 [f67ccb44] HDF5 v0.17.2 [3e5b6fbb] HostCPUFeatures v0.1.18 [34004b35] HypergeometricFunctions v0.3.28 [615f187c] IfElse v0.1.1 [92d709cd] IrrationalConstants v0.2.6 [692b3bcd] JLLWrappers v1.7.1 [10f19ff3] LayoutPointers v0.1.17 [2ab3a3ac] LogExpFunctions v0.3.29 [bdcacae8] LoopVectorization v0.12.173 [3da0fdf6] MPIPreferences v0.1.11 [d125e4d3] ManualMemory v0.1.8 [e1d29d7a] Missings v1.2.0 [b8a86587] NearestNeighbors v0.4.26 [6fe1bfb0] OffsetArrays v1.17.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.36 [1d0040c9] PolyesterWeave v0.2.2 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [49802e3a] ProgressBars v1.5.1 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [bf1adee6] RedClust v1.2.2 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [94e857df] SIMDTypes v0.1.0 [476501e8] SLEEFPirates v0.6.43 [431bcebd] SciMLPublic v1.0.0 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [aedffcd0] Static v1.3.1 [0d7ed370] StaticArrayInterface v1.8.0 [90137ffa] StaticArrays v1.9.15 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.9 [4c63d2b9] StatsFuns v1.5.2 [8290d209] ThreadingUtilities v0.5.5 [3a884ed6] UnPack v1.0.2 [3d5dd08c] VectorizationBase v0.21.72 ⌅ [0234f1f7] HDF5_jll v1.14.6+0 [e33a78d0] Hwloc_jll v2.12.2+0 [94ce4f54] Libiconv_jll v1.18.0+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 v2.13.9+0 [a65dc6b1] Xorg_libpciaccess_jll v0.18.1+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 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [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 v1.14.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [4607b0f0] SuiteSparse [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 v1.9.2+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [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 ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... PriorHyperparamsList(1.0, 18.944772421000895, 1.0, 1.0, 93776.62348395443, 8671.323180508774, 0.47502686811017075, 2.2747717749416183, 0.40272790925167, 0.4867096648246321, 2.1309944566131516, 100, true, 0)Model Hyperparameters Likelihood Hyperparameters δ₁ = 1.000 δ₂ = 18.945 α = 1.000 β = 1.000 ζ = 93776.623 γ = 8671.323 Partition Prior Hyperparameters η = 4.750e-01 σ = 2.275 u = 4.867e-01 v = 2.131 Miscellaneous Hyperparameters Proposal standard deviation for sampling r = 4.027e-01 Repulsion is enabled? true Maximum number of clusters = none Initial number of clusters = 100 MCMC data : 100×100 dissimilarity matrix. MCMC data : 100×100 dissimilarity matrix. MCMCOptionsList(5000, 1000, 1, 5, 0, 4000)MCMC Options 5000 iterations 1000 burnin iterations 4000 samples 5 restricted Gibbs steps per split-merge step 0 split-merge steps per iteration MCMC result with 4000 samples MCMC Summary General 5000 iterations 1000 iterations discarded as burnin 4000 samples 5 restricted Gibbs steps per split-merge step 0 split-merge steps per iteration Acceptance rate for split-merge steps = 0.000e+00 Acceptance rate for sampling r = 5.208e-01 Using repulsion: true Maximum number of clusters allowed: any Runtime = 4.40 s Time per iteration : 879.01 μs Summary for K IAC : 1.938 ESS : 2063.957 ESS per sample : 5.160e-01 Posterior mean : 10.005 Posterior variance : 4.976e-03 Summary for r IAC : 12.417 ESS : 322.150 ESS per sample : 8.054e-02 Posterior mean : 3.967 Posterior variance : 1.053 Summary for p IAC : 9.310 ESS : 429.635 ESS per sample : 1.074e-01 Posterior mean : 6.867e-01 Posterior variance : 3.298e-03 Test Summary: | Pass Total Time master | 83 83 3m35.0s Testing RedClust tests passed Testing completed after 519.39s PkgEval succeeded after 584.13s