Package evaluation to test SimSearchManifoldLearning on Julia 1.14.0-DEV.1441 (812f3beb0a*) started at 2025-12-30T19:22:58.408 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 9.87s ################################################################################ # Installation # Installing SimSearchManifoldLearning... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [ca7ab67e] + SimSearchManifoldLearning v0.3.2 Updating `~/.julia/environments/v1.14/Manifest.toml` [47edcb42] + ADTypes v1.21.0 [7d9f7c33] + Accessors v0.1.43 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [ec485272] + ArnoldiMethod v0.4.0 [7d9fca2a] + Arpack v0.5.4 [4fba245c] + ArrayInterface v7.22.0 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [2a0fbf3d] + CPUSummary v0.2.7 [fb6a15b2] + CloseOpenIntervals v0.1.13 [861a8166] + Combinatorics v1.1.0 [bbf7d656] + CommonSubexpressions v0.3.1 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [9a962f9c] + DataAPI v1.16.0 ⌅ [864edb3b] + DataStructures v0.18.22 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [a0c0ee7d] + DifferentiationInterface v0.7.13 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.15.0 [6a86dc24] + FiniteDiff v2.29.0 ⌅ [f6369f11] + ForwardDiff v0.10.39 ⌃ [86223c79] + Graphs v1.13.1 [34004b35] + HypergeometricFunctions v0.3.28 [615f187c] + IfElse v0.1.1 [d25df0c9] + Inflate v0.1.5 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.7.1 [10f19ff3] + LayoutPointers v0.1.17 [2ab3a3ac] + LogExpFunctions v0.3.29 ⌅ [2fda8390] + LsqFit v0.12.1 [1914dd2f] + MacroTools v0.5.16 [06eb3307] + ManifoldLearning v0.9.0 [d125e4d3] + ManualMemory v0.1.8 [e1d29d7a] + Missings v1.2.0 ⌅ [6f286f6a] + MultivariateStats v0.9.0 [d41bc354] + NLSolversBase v7.10.0 [77ba4419] + NaNMath v1.1.3 [87e2bd06] + OptimBase v2.0.2 [bac558e1] + OrderedCollections v1.8.1 ⌃ [90014a1f] + PDMats v0.11.35 [d96e819e] + Parameters v0.12.3 [f517fe37] + Polyester v0.7.18 [1d0040c9] + PolyesterWeave v0.2.2 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [94e857df] + SIMDTypes v0.1.0 [431bcebd] + SciMLPublic v1.0.1 ⌅ [0e966ebe] + SearchModels v0.4.1 [efcf1570] + Setfield v1.1.2 [ca7ab67e] + SimSearchManifoldLearning v0.3.2 [053f045d] + SimilaritySearch v0.13.7 [699a6c99] + SimpleTraits v0.9.5 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [aedffcd0] + Static v1.3.1 [0d7ed370] + StaticArrayInterface v1.8.0 [90137ffa] + StaticArrays v1.9.16 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 ⌅ [2913bbd2] + StatsBase v0.33.21 [4c63d2b9] + StatsFuns v1.5.2 [7792a7ef] + StrideArraysCore v0.5.8 [8290d209] + ThreadingUtilities v0.5.5 [3a884ed6] + UnPack v1.0.2 ⌅ [68821587] + Arpack_jll v3.5.2+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [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 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [8e850b90] + libblastrampoline_jll v5.15.0+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` Installation completed after 6.66s ################################################################################ # 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:585 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:585 Precompilation failed after 13.84s ################################################################################ # Testing # Testing SimSearchManifoldLearning Status `/tmp/jl_8PTB5t/Project.toml` [7d9fca2a] Arpack v0.5.4 [b4f34e82] Distances v0.10.12 ⌅ [2fda8390] LsqFit v0.12.1 [06eb3307] ManifoldLearning v0.9.0 [f517fe37] Polyester v0.7.18 [ca7ab67e] SimSearchManifoldLearning v0.3.2 [053f045d] SimilaritySearch v0.13.7 [82ae8749] StatsAPI v1.8.0 [37e2e46d] LinearAlgebra v1.13.0 [9a3f8284] Random v1.11.0 [2f01184e] SparseArrays v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_8PTB5t/Manifest.toml` [47edcb42] ADTypes v1.21.0 [7d9f7c33] Accessors v0.1.43 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [ec485272] ArnoldiMethod v0.4.0 [7d9fca2a] Arpack v0.5.4 [4fba245c] ArrayInterface v7.22.0 [62783981] BitTwiddlingConvenienceFunctions v0.1.6 [2a0fbf3d] CPUSummary v0.2.7 [fb6a15b2] CloseOpenIntervals v0.1.13 [861a8166] Combinatorics v1.1.0 [bbf7d656] CommonSubexpressions v0.3.1 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [adafc99b] CpuId v0.3.1 [9a962f9c] DataAPI v1.16.0 ⌅ [864edb3b] DataStructures v0.18.22 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [a0c0ee7d] DifferentiationInterface v0.7.13 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [1a297f60] FillArrays v1.15.0 [6a86dc24] FiniteDiff v2.29.0 ⌅ [f6369f11] ForwardDiff v0.10.39 ⌃ [86223c79] Graphs v1.13.1 [34004b35] HypergeometricFunctions v0.3.28 [615f187c] IfElse v0.1.1 [d25df0c9] Inflate v0.1.5 [3587e190] InverseFunctions v0.1.17 [92d709cd] IrrationalConstants v0.2.6 [692b3bcd] JLLWrappers v1.7.1 [10f19ff3] LayoutPointers v0.1.17 [2ab3a3ac] LogExpFunctions v0.3.29 ⌅ [2fda8390] LsqFit v0.12.1 [1914dd2f] MacroTools v0.5.16 [06eb3307] ManifoldLearning v0.9.0 [d125e4d3] ManualMemory v0.1.8 [e1d29d7a] Missings v1.2.0 ⌅ [6f286f6a] MultivariateStats v0.9.0 [d41bc354] NLSolversBase v7.10.0 [77ba4419] NaNMath v1.1.3 [87e2bd06] OptimBase v2.0.2 [bac558e1] OrderedCollections v1.8.1 ⌃ [90014a1f] PDMats v0.11.35 [d96e819e] Parameters v0.12.3 [f517fe37] Polyester v0.7.18 [1d0040c9] PolyesterWeave v0.2.2 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.1 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [94e857df] SIMDTypes v0.1.0 [431bcebd] SciMLPublic v1.0.1 ⌅ [0e966ebe] SearchModels v0.4.1 [efcf1570] Setfield v1.1.2 [ca7ab67e] SimSearchManifoldLearning v0.3.2 [053f045d] SimilaritySearch v0.13.7 [699a6c99] SimpleTraits v0.9.5 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [aedffcd0] Static v1.3.1 [0d7ed370] StaticArrayInterface v1.8.0 [90137ffa] StaticArrays v1.9.16 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 ⌅ [2913bbd2] StatsBase v0.33.21 [4c63d2b9] StatsFuns v1.5.2 [7792a7ef] StrideArraysCore v0.5.8 [8290d209] ThreadingUtilities v0.5.5 [3a884ed6] UnPack v1.0.2 ⌅ [68821587] Arpack_jll v3.5.2+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [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 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [1a1011a3] SharedArrays v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [8e850b90] libblastrampoline_jll v5.15.0+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... 1.406429 seconds (869.04 k allocations: 43.901 MiB, 97.60% compilation time) LOG add_vertex! sp=1 ep=1 n=1 BeamSearch BeamSearch(bsize=4, Δ=1.0, maxvisits=1000000) 2025-12-30T19:25:24.597 LOG n.size quantiles:[0.0, 0.0, 0.0, 0.0, 0.0] LOG add_vertex! sp=2 ep=2 n=2 BeamSearch BeamSearch(bsize=4, Δ=1.0, maxvisits=1000000) 2025-12-30T19:25:26.220 LOG n.size quantiles:[1.0, 1.0, 1.0, 1.0, 1.0] LOG add_vertex! sp=295 ep=299 n=294 BeamSearch BeamSearch(bsize=2, Δ=0.7619048, maxvisits=114) 2025-12-30T19:25:34.946 LOG n.size quantiles:[3.0, 3.0, 3.0, 3.0, 3.0] 0.279341 seconds (252.49 k allocations: 12.447 MiB, 98.12% compilation time) 0.521342 seconds (441.23 k allocations: 22.799 MiB, 94.71% compilation time) LOG add_vertex! sp=1 ep=1 n=1 BeamSearch BeamSearch(bsize=4, Δ=1.0, maxvisits=1000000) 2025-12-30T19:25:44.062 LOG n.size quantiles:[0.0, 0.0, 0.0, 0.0, 0.0] LOG add_vertex! sp=295 ep=299 n=294 BeamSearch BeamSearch(bsize=2, Δ=0.6715938, maxvisits=120) 2025-12-30T19:25:47.810 LOG n.size quantiles:[3.0, 3.0, 3.0, 3.0, 4.0] 0.299866 seconds (252.47 k allocations: 12.449 MiB, 98.11% compilation time) Test Summary: | Pass Total Time SimilaritySearch for ManifoldLearning api | 4 4 1m01.6s Test Summary: | Pass Total Time utils tests | 3 3 3.6s 0.262796 seconds (178.89 k allocations: 9.027 MiB, 99.94% compilation time) 0.000056 seconds (18 allocations: 1.125 KiB) 0.046114 seconds (3.75 k allocations: 194.273 KiB, 98.27% compilation time) *** computing graph *** layout embedding RandomLayout *** fit ab / embedding *** opt embedding UMAP construction time cost report: - fuzzy graph: 0.39194514 - embedding init: 7.53e-6 - embedding opt: 0.048612679 0.284126 seconds (168.46 k allocations: 8.662 MiB, 99.65% compilation time) *** computing graph *** layout embedding RandomLayout *** fit ab / embedding *** opt embedding UMAP construction time cost report: - fuzzy graph: 0.000744573 - embedding init: 6.38e-6 - embedding opt: 0.050025436 0.000562 seconds (132 allocations: 21.133 KiB) *** computing graph *** layout embedding RandomLayout *** fit ab / embedding *** opt embedding UMAP construction time cost report: - fuzzy graph: 0.000729303 - embedding init: 3.55e-6 - embedding opt: 0.048759437 0.000594 seconds (132 allocations: 21.133 KiB) *** computing graph *** layout embedding SpectralLayout *** fit ab / embedding *** opt embedding UMAP construction time cost report: - fuzzy graph: 0.000732863 - embedding init: 3.66245981 - embedding opt: 0.049694809 0.000675 seconds (132 allocations: 21.133 KiB) *** computing graph *** layout embedding PrecomputedLayout *** fit ab / embedding *** opt embedding UMAP construction time cost report: - fuzzy graph: 0.000836402 - embedding init: 3.8e-7 - embedding opt: 0.048613279 0.000600 seconds (132 allocations: 21.133 KiB) *** computing graph *** layout embedding KnnGraphLayout *** fit ab / embedding *** opt embedding UMAP construction time cost report: - fuzzy graph: 0.000775963 - embedding init: 2.8709e-5 - embedding opt: 0.048891236 0.000607 seconds (132 allocations: 21.133 KiB) *** computing graph *** layout embedding RandomLayout *** fit ab / embedding *** opt embedding UMAP construction time cost report: - fuzzy graph: 0.000794393 - embedding init: 2.74e-6 - embedding opt: 0.048994515 0.000597 seconds (132 allocations: 21.133 KiB) *** computing graph *** layout embedding RandomLayout *** fit ab / embedding *** opt embedding UMAP construction time cost report: - fuzzy graph: 0.000805803 - embedding init: 3.89e-6 - embedding opt: 0.049324162 0.000636 seconds (132 allocations: 21.133 KiB) *** computing graph *** layout embedding RandomLayout *** fit ab / embedding *** opt embedding UMAP construction time cost report: - fuzzy graph: 0.000759573 - embedding init: 5.01e-6 - embedding opt: 0.04840046 0.000564 seconds (132 allocations: 21.133 KiB) *** computing graph *** layout embedding RandomLayout *** fit ab / embedding *** opt embedding UMAP construction time cost report: - fuzzy graph: 0.000736703 - embedding init: 3.91e-6 - embedding opt: 0.045643416 (rhos, sigmas) = (Float32[1.0, 2.0, 3.0], Float32[1.9829102, 2.5358887, 2.6249695]) ┌ Info: [2.321931655873457, 2.321930914055594, 2.3219283113392373] │ diffs = │ 3-element Vector{Float64}: │ 3.560986094885976e-6 │ 2.819168231749103e-6 └ 2.164518750902289e-7 (:last => rhos, sigmas) = (:last => Float32[0.0, 1.0, 2.0], Float32[5.421011f-20, 5.421011f-20, 5.421011f-20]) (rows, cols, vals) = (Int32[2, 1, 2], Int32[1, 2, 3], Float32[1.0, 1.0, 1.0]) [ Info: spectral_layout! [ Info: initialize_embedding [ Info: Matrix{Float32} => Matrix{Float32} [ Info: ===== umap predict ===== 0.000119 seconds (55 allocations: 4.297 KiB) *** computing graph *** layout embedding SpectralLayout ┌ Info: Arpack.XYAUPD_Exception(1) └ Error encountered in spectral_layout; defaulting to random layout *** fit ab / embedding *** opt embedding UMAP construction time cost report: - fuzzy graph: 5.7199e-5 - embedding init: 0.098558754 - embedding opt: 5.5109e-5 0.000112 seconds (55 allocations: 4.297 KiB) *** computing graph *** layout embedding SpectralLayout ┌ Info: Arpack.XYAUPD_Exception(1) └ Error encountered in spectral_layout; defaulting to random layout *** fit ab / embedding *** opt embedding UMAP construction time cost report: - fuzzy graph: 5.358e-5 - embedding init: 0.003279209 - embedding opt: 5.7479e-5 0.000154 seconds (55 allocations: 4.297 KiB) *** computing graph *** layout embedding SpectralLayout ┌ Info: Arpack.XYAUPD_Exception(1) └ Error encountered in spectral_layout; defaulting to random layout *** fit ab / embedding *** opt embedding UMAP construction time cost report: - fuzzy graph: 5.595e-5 - embedding init: 0.003485098 - embedding opt: 5.805e-5 Test Summary: | Pass Total Time umap tests | 44 44 1m09.1s Testing SimSearchManifoldLearning tests passed Testing completed after 212.86s PkgEval succeeded after 258.66s