Package evaluation of SimSearchManifoldLearning on Julia 1.13.0-DEV.1222 (39e1473f3b*) started at 2025-09-30T22:46:34.519


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 9.41s


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

Installing SimSearchManifoldLearning...
   Resolving package versions...
    Updating `~/.julia/environments/v1.13/Project.toml`
  [ca7ab67e] + SimSearchManifoldLearning v0.3.2
    Updating `~/.julia/environments/v1.13/Manifest.toml`
  [47edcb42] + ADTypes v1.18.0
  [7d9f7c33] + Accessors v0.1.42
  [79e6a3ab] + Adapt v4.4.0
  [66dad0bd] + AliasTables v1.1.3
  [ec485272] + ArnoldiMethod v0.4.0
  [7d9fca2a] + Arpack v0.5.4
  [4fba245c] + ArrayInterface v7.20.0
  [62783981] + BitTwiddlingConvenienceFunctions v0.1.6
  [2a0fbf3d] + CPUSummary v0.2.7
  [fb6a15b2] + CloseOpenIntervals v0.1.13
  [da1fd8a2] + CodeTracking v2.0.1
  [861a8166] + Combinatorics v1.0.3
  [bbf7d656] + CommonSubexpressions v0.3.1
  [f70d9fcc] + CommonWorldInvalidations v1.0.0
  [34da2185] + Compat v4.18.0
  [807dbc54] + Compiler v0.1.1
  [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 v0.7.8
  [b4f34e82] + Distances v0.10.12
  [31c24e10] + Distributions v0.25.120
  [ffbed154] + DocStringExtensions v0.9.5
  [5789e2e9] + FileIO v1.17.0
  [1a297f60] + FillArrays v1.14.0
  [6a86dc24] + FiniteDiff v2.28.1
⌅ [f6369f11] + ForwardDiff v0.10.39
  [86223c79] + Graphs v1.13.1
  [076d061b] + HashArrayMappedTries v0.2.0
  [34004b35] + HypergeometricFunctions v0.3.28
  [615f187c] + IfElse v0.1.1
  [d25df0c9] + Inflate v0.1.5
  [3587e190] + InverseFunctions v0.1.17
  [92d709cd] + IrrationalConstants v0.2.4
  [c3a54625] + JET v0.10.7
⌅ [033835bb] + JLD2 v0.5.15
  [692b3bcd] + JLLWrappers v1.7.1
  [aa1ae85d] + JuliaInterpreter v0.10.5
  [70703baa] + JuliaSyntax v1.0.2
  [10f19ff3] + LayoutPointers v0.1.17
  [2ab3a3ac] + LogExpFunctions v0.3.29
  [6f1432cf] + LoweredCodeUtils v3.4.4
⌅ [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 v1.5.0
  [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 v0.8.0
  [94e857df] + SIMDTypes v0.1.0
  [431bcebd] + SciMLPublic v1.0.0
  [7e506255] + ScopedValues v1.5.0
  [0e966ebe] + SearchModels v0.4.1
  [efcf1570] + Setfield v1.1.2
  [ca7ab67e] + SimSearchManifoldLearning v0.3.2
  [053f045d] + SimilaritySearch v0.13.0
  [699a6c99] + SimpleTraits v0.9.5
  [a2af1166] + SortingAlgorithms v1.2.2
  [276daf66] + SpecialFunctions v2.5.1
  [aedffcd0] + Static v1.3.0
  [0d7ed370] + StaticArrayInterface v1.8.0
  [90137ffa] + StaticArrays v1.9.15
  [1e83bf80] + StaticArraysCore v1.4.3
  [10745b16] + Statistics v1.11.1
  [82ae8749] + StatsAPI v1.7.1
⌅ [2913bbd2] + StatsBase v0.33.21
  [4c63d2b9] + StatsFuns v1.5.0
  [7792a7ef] + StrideArraysCore v0.5.8
  [8290d209] + ThreadingUtilities v0.5.5
  [3bb67fe8] + TranscodingStreams v0.11.3
  [3a884ed6] + UnPack v1.0.2
⌅ [68821587] + Arpack_jll v3.5.1+1
  [efe28fd5] + OpenSpecFun_jll v0.5.6+0
  [f50d1b31] + Rmath_jll v0.5.1+0
  [0dad84c5] + ArgTools v1.1.2
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates v1.11.0
  [8ba89e20] + Distributed 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
  [b27032c2] + LibCURL v0.6.4
  [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
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization v1.11.0
  [1a1011a3] + SharedArrays v1.11.0
  [6462fe0b] + Sockets v1.11.0
  [2f01184e] + SparseArrays v1.13.0
  [f489334b] + StyledStrings v1.11.0
  [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 v8.16.0+0
  [e37daf67] + LibGit2_jll v1.9.1+0
  [29816b5a] + LibSSH2_jll v1.11.3+1
  [14a3606d] + MozillaCACerts_jll v2025.9.9
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [05823500] + OpenLibm_jll v0.8.7+0
  [458c3c95] + OpenSSL_jll v3.5.2+0
  [efcefdf7] + PCRE2_jll v10.46.0+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 v5.13.1+0
  [8e850ede] + nghttp2_jll v1.67.1+0
  [3f19e933] + p7zip_jll v17.6.0+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 6.63s


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# Precompilation
#

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 438.61s


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

     Testing SimSearchManifoldLearning
      Status `/tmp/jl_EMJjeg/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 v0.13.0
  [82ae8749] StatsAPI v1.7.1
  [37e2e46d] LinearAlgebra v1.13.0
  [9a3f8284] Random v1.11.0
  [2f01184e] SparseArrays v1.13.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_EMJjeg/Manifest.toml`
  [47edcb42] ADTypes v1.18.0
  [7d9f7c33] Accessors v0.1.42
  [79e6a3ab] Adapt v4.4.0
  [66dad0bd] AliasTables v1.1.3
  [ec485272] ArnoldiMethod v0.4.0
  [7d9fca2a] Arpack v0.5.4
  [4fba245c] ArrayInterface v7.20.0
  [62783981] BitTwiddlingConvenienceFunctions v0.1.6
  [2a0fbf3d] CPUSummary v0.2.7
  [fb6a15b2] CloseOpenIntervals v0.1.13
  [da1fd8a2] CodeTracking v2.0.1
  [861a8166] Combinatorics v1.0.3
  [bbf7d656] CommonSubexpressions v0.3.1
  [f70d9fcc] CommonWorldInvalidations v1.0.0
  [34da2185] Compat v4.18.0
  [807dbc54] Compiler v0.1.1
  [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 v0.7.8
  [b4f34e82] Distances v0.10.12
  [31c24e10] Distributions v0.25.120
  [ffbed154] DocStringExtensions v0.9.5
  [5789e2e9] FileIO v1.17.0
  [1a297f60] FillArrays v1.14.0
  [6a86dc24] FiniteDiff v2.28.1
⌅ [f6369f11] ForwardDiff v0.10.39
  [86223c79] Graphs v1.13.1
  [076d061b] HashArrayMappedTries v0.2.0
  [34004b35] HypergeometricFunctions v0.3.28
  [615f187c] IfElse v0.1.1
  [d25df0c9] Inflate v0.1.5
  [3587e190] InverseFunctions v0.1.17
  [92d709cd] IrrationalConstants v0.2.4
  [c3a54625] JET v0.10.7
⌅ [033835bb] JLD2 v0.5.15
  [692b3bcd] JLLWrappers v1.7.1
  [aa1ae85d] JuliaInterpreter v0.10.5
  [70703baa] JuliaSyntax v1.0.2
  [10f19ff3] LayoutPointers v0.1.17
  [2ab3a3ac] LogExpFunctions v0.3.29
  [6f1432cf] LoweredCodeUtils v3.4.4
⌅ [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 v1.5.0
  [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 v0.8.0
  [94e857df] SIMDTypes v0.1.0
  [431bcebd] SciMLPublic v1.0.0
  [7e506255] ScopedValues v1.5.0
  [0e966ebe] SearchModels v0.4.1
  [efcf1570] Setfield v1.1.2
  [ca7ab67e] SimSearchManifoldLearning v0.3.2
  [053f045d] SimilaritySearch v0.13.0
  [699a6c99] SimpleTraits v0.9.5
  [a2af1166] SortingAlgorithms v1.2.2
  [276daf66] SpecialFunctions v2.5.1
  [aedffcd0] Static v1.3.0
  [0d7ed370] StaticArrayInterface v1.8.0
  [90137ffa] StaticArrays v1.9.15
  [1e83bf80] StaticArraysCore v1.4.3
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.7.1
⌅ [2913bbd2] StatsBase v0.33.21
  [4c63d2b9] StatsFuns v1.5.0
  [7792a7ef] StrideArraysCore v0.5.8
  [8290d209] ThreadingUtilities v0.5.5
  [3bb67fe8] TranscodingStreams v0.11.3
  [3a884ed6] UnPack v1.0.2
⌅ [68821587] Arpack_jll v3.5.1+1
  [efe28fd5] OpenSpecFun_jll v0.5.6+0
  [f50d1b31] Rmath_jll v0.5.1+0
  [0dad84c5] ArgTools v1.1.2
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [8ba89e20] Distributed 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
  [b27032c2] LibCURL v0.6.4
  [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
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization v1.11.0
  [1a1011a3] SharedArrays v1.11.0
  [6462fe0b] Sockets v1.11.0
  [2f01184e] SparseArrays v1.13.0
  [f489334b] StyledStrings v1.11.0
  [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 v8.16.0+0
  [e37daf67] LibGit2_jll v1.9.1+0
  [29816b5a] LibSSH2_jll v1.11.3+1
  [14a3606d] MozillaCACerts_jll v2025.9.9
  [4536629a] OpenBLAS_jll v0.3.29+0
  [05823500] OpenLibm_jll v0.8.7+0
  [458c3c95] OpenSSL_jll v3.5.2+0
  [efcefdf7] PCRE2_jll v10.46.0+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 v5.13.1+0
  [8e850ede] nghttp2_jll v1.67.1+0
  [3f19e933] p7zip_jll v17.6.0+0
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading.
     Testing Running tests...
Precompiling packages...
   7077.5 ms  ✓ Distributions → DistributionsTestExt
  1 dependency successfully precompiled in 9 seconds. 49 already precompiled.
  1.674859 seconds (873.68 k allocations: 46.256 MiB, 15.04% gc time, 96.87% compilation time)
LOG add_vertex! sp=1 ep=1 n=1 BeamSearch(bsize=4, Δ=1.0, maxvisits=1000000) 2025-09-30T22:55:56.199
LOG n.size quantiles:[0.0, 0.0, 0.0, 0.0, 0.0]
LOG add_vertex! sp=2 ep=2 n=2 BeamSearch(bsize=4, Δ=1.0, maxvisits=1000000) 2025-09-30T22:55:57.305
LOG n.size quantiles:[1.0, 1.0, 1.0, 1.0, 1.0]
LOG add_vertex! sp=295 ep=299 n=294 BeamSearch(bsize=11, Δ=0.92, maxvisits=120) 2025-09-30T22:56:06.237
LOG n.size quantiles:[1.0, 2.0, 2.0, 2.0, 3.0]
  0.236681 seconds (256.88 k allocations: 13.222 MiB, 96.67% compilation time)
  0.554454 seconds (449.90 k allocations: 24.306 MiB, 92.72% compilation time)
LOG add_vertex! sp=1 ep=1 n=1 BeamSearch(bsize=4, Δ=1.0, maxvisits=1000000) 2025-09-30T22:56:15.569
LOG n.size quantiles:[0.0, 0.0, 0.0, 0.0, 0.0]
LOG add_vertex! sp=295 ep=299 n=294 BeamSearch(bsize=6, Δ=1.155, maxvisits=114) 2025-09-30T22:56:19.708
LOG n.size quantiles:[2.0, 2.0, 2.0, 2.0, 2.0]
  0.233969 seconds (256.87 k allocations: 13.225 MiB, 97.35% compilation time)
Test Summary:                             | Pass  Total     Time
SimilaritySearch for ManifoldLearning api |    4      4  1m04.8s
Test Summary: | Pass  Total  Time
utils tests   |    3      3  4.0s
  0.191476 seconds (177.64 k allocations: 9.395 MiB, 99.90% compilation time)
  0.000046 seconds (18 allocations: 1.125 KiB)
  0.036220 seconds (3.80 k allocations: 212.320 KiB, 96.60% compilation time)
*** computing graph
*** layout embedding RandomLayout
*** fit ab / embedding
*** opt embedding
UMAP construction time cost report:
- fuzzy graph: 0.731478221
- embedding init: 4.72e-6
- embedding opt: 0.044150875

  0.254753 seconds (166.87 k allocations: 8.988 MiB, 99.56% compilation time)
*** computing graph
*** layout embedding RandomLayout
*** fit ab / embedding
*** opt embedding
UMAP construction time cost report:
- fuzzy graph: 0.000747503
- embedding init: 3.33e-6
- embedding opt: 0.04785454

  0.000979 seconds (132 allocations: 21.133 KiB)
*** computing graph
*** layout embedding RandomLayout
*** fit ab / embedding
*** opt embedding
UMAP construction time cost report:
- fuzzy graph: 0.000735843
- embedding init: 3.07e-6
- embedding opt: 0.044914088

  0.001016 seconds (132 allocations: 21.133 KiB)
*** computing graph
*** layout embedding SpectralLayout
*** fit ab / embedding
*** opt embedding
UMAP construction time cost report:
- fuzzy graph: 0.000817062
- embedding init: 4.879928309
- embedding opt: 0.034655817

  0.001054 seconds (132 allocations: 21.133 KiB)
*** computing graph
*** layout embedding PrecomputedLayout
*** fit ab / embedding
*** opt embedding
UMAP construction time cost report:
- fuzzy graph: 0.000819812
- embedding init: 3.2e-7
- embedding opt: 0.044603461

  0.001047 seconds (132 allocations: 21.133 KiB)
*** computing graph
*** layout embedding KnnGraphLayout
*** fit ab / embedding
*** opt embedding
UMAP construction time cost report:
- fuzzy graph: 0.000834532
- embedding init: 3.986e-5
- embedding opt: 0.043957177

  0.001014 seconds (132 allocations: 21.133 KiB)
*** computing graph
*** layout embedding RandomLayout
*** fit ab / embedding
*** opt embedding
UMAP construction time cost report:
- fuzzy graph: 0.000844441
- embedding init: 2.34e-6
- embedding opt: 0.040725818

  0.001046 seconds (132 allocations: 21.133 KiB)
*** computing graph
*** layout embedding RandomLayout
*** fit ab / embedding
*** opt embedding
UMAP construction time cost report:
- fuzzy graph: 0.000809412
- embedding init: 3.86e-6
- embedding opt: 0.052739753

  0.001661 seconds (132 allocations: 21.133 KiB)
*** computing graph
*** layout embedding RandomLayout
*** fit ab / embedding
*** opt embedding
UMAP construction time cost report:
- fuzzy graph: 0.00109328
- embedding init: 5.64e-6
- embedding opt: 0.065933586

  0.001652 seconds (132 allocations: 21.133 KiB)
*** computing graph
*** layout embedding RandomLayout
*** fit ab / embedding
*** opt embedding
UMAP construction time cost report:
- fuzzy graph: 0.0010605
- embedding init: 4.19e-6
- embedding opt: 0.06027619

(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 =====
  0.000226 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: 8.4449e-5
- embedding init: 0.098580511
- embedding opt: 7.14e-5

  0.000190 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: 6.8619e-5
- embedding init: 0.003420637
- embedding opt: 6.7199e-5

  0.000201 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: 7.0109e-5
- embedding init: 0.003508236
- embedding opt: 7.3989e-5

Test Summary: | Pass  Total     Time
umap tests    |   44     44  1m26.7s
     Testing SimSearchManifoldLearning tests passed 

Testing completed after 186.19s

PkgEval succeeded after 689.24s