Package evaluation of UMAP on Julia 1.12.0-rc1.2 (995ff9db19*) started at 2025-07-14T18:38:48.741


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 8.54s


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

Installing UMAP...
   Resolving package versions...
    Updating `~/.julia/environments/v1.12/Project.toml`
  [c4f8c510] + UMAP v0.1.11
    Updating `~/.julia/environments/v1.12/Manifest.toml`
  [47edcb42] + ADTypes v1.15.0
  [79e6a3ab] + Adapt v4.3.0
  [66dad0bd] + AliasTables v1.1.3
  [ec485272] + ArnoldiMethod v0.4.0
  [7d9fca2a] + Arpack v0.5.4
  [4fba245c] + ArrayInterface v7.19.0
  [bbf7d656] + CommonSubexpressions v0.3.1
  [34da2185] + Compat v4.17.0
  [187b0558] + ConstructionBase v1.6.0
  [9a962f9c] + DataAPI v1.16.0
  [864edb3b] + DataStructures v0.18.22
  [163ba53b] + DiffResults v1.1.0
  [b552c78f] + DiffRules v1.15.1
  [a0c0ee7d] + DifferentiationInterface v0.7.2
  [b4f34e82] + Distances v0.10.12
  [31c24e10] + Distributions v0.25.120
  [ffbed154] + DocStringExtensions v0.9.5
  [1a297f60] + FillArrays v1.13.0
  [6a86dc24] + FiniteDiff v2.27.0
  [f6369f11] + ForwardDiff v1.0.1
  [86223c79] + Graphs v1.13.0
  [34004b35] + HypergeometricFunctions v0.3.28
  [d25df0c9] + Inflate v0.1.5
  [92d709cd] + IrrationalConstants v0.2.4
  [692b3bcd] + JLLWrappers v1.7.0
  [2ab3a3ac] + LogExpFunctions v0.3.29
  [2fda8390] + LsqFit v0.15.1
  [1914dd2f] + MacroTools v0.5.16
  [e1d29d7a] + Missings v1.2.0
  [d41bc354] + NLSolversBase v7.10.0
  [77ba4419] + NaNMath v1.1.3
  [dd2c4c9e] + NearestNeighborDescent v0.3.7
  [bac558e1] + OrderedCollections v1.8.1
  [90014a1f] + PDMats v0.11.35
  [aea7be01] + PrecompileTools v1.3.2
  [21216c6a] + Preferences v1.4.3
  [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
  [efcf1570] + Setfield v1.1.2
  [699a6c99] + SimpleTraits v0.9.4
  [a2af1166] + SortingAlgorithms v1.2.1
  [276daf66] + SpecialFunctions v2.5.1
  [90137ffa] + StaticArrays v1.9.13
  [1e83bf80] + StaticArraysCore v1.4.3
  [10745b16] + Statistics v1.11.1
  [82ae8749] + StatsAPI v1.7.1
  [2913bbd2] + StatsBase v0.34.5
  [4c63d2b9] + StatsFuns v1.5.0
  [c4f8c510] + UMAP v0.1.11
⌅ [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 v1.6.0
  [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 v1.12.0
  [56ddb016] + Logging v1.11.0
  [d6f4376e] + Markdown v1.11.0
  [a63ad114] + Mmap v1.11.0
  [ca575930] + NetworkOptions v1.3.0
  [44cfe95a] + Pkg v1.13.0
  [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 v1.12.0
  [f489334b] + StyledStrings v1.11.0
  [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 v8.11.1+1
  [e37daf67] + LibGit2_jll v1.9.0+0
  [29816b5a] + LibSSH2_jll v1.11.3+1
  [14a3606d] + MozillaCACerts_jll v2025.5.20
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [05823500] + OpenLibm_jll v0.8.5+0
  [458c3c95] + OpenSSL_jll v3.5.1+0
  [bea87d4a] + SuiteSparse_jll v7.8.3+2
  [83775a58] + Zlib_jll v1.3.1+2
  [8e850b90] + libblastrampoline_jll v5.13.1+0
  [8e850ede] + nghttp2_jll v1.64.0+1
  [3f19e933] + p7zip_jll v17.5.0+2
        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 4.38s


################################################################################
# Precompilation
#

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 93.06s


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

     Testing UMAP
      Status `/tmp/jl_ChIoYu/Project.toml`
  [7d9fca2a] Arpack v0.5.4
  [b4f34e82] Distances v0.10.12
  [2fda8390] LsqFit v0.15.1
  [dd2c4c9e] NearestNeighborDescent v0.3.7
  [c4f8c510] UMAP v0.1.11
  [37e2e46d] LinearAlgebra v1.12.0
  [9a3f8284] Random v1.11.0
  [2f01184e] SparseArrays v1.12.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_ChIoYu/Manifest.toml`
  [47edcb42] ADTypes v1.15.0
  [79e6a3ab] Adapt v4.3.0
  [66dad0bd] AliasTables v1.1.3
  [ec485272] ArnoldiMethod v0.4.0
  [7d9fca2a] Arpack v0.5.4
  [4fba245c] ArrayInterface v7.19.0
  [bbf7d656] CommonSubexpressions v0.3.1
  [34da2185] Compat v4.17.0
  [187b0558] ConstructionBase v1.6.0
  [9a962f9c] DataAPI v1.16.0
  [864edb3b] DataStructures v0.18.22
  [163ba53b] DiffResults v1.1.0
  [b552c78f] DiffRules v1.15.1
  [a0c0ee7d] DifferentiationInterface v0.7.2
  [b4f34e82] Distances v0.10.12
  [31c24e10] Distributions v0.25.120
  [ffbed154] DocStringExtensions v0.9.5
  [1a297f60] FillArrays v1.13.0
  [6a86dc24] FiniteDiff v2.27.0
  [f6369f11] ForwardDiff v1.0.1
  [86223c79] Graphs v1.13.0
  [34004b35] HypergeometricFunctions v0.3.28
  [d25df0c9] Inflate v0.1.5
  [92d709cd] IrrationalConstants v0.2.4
  [692b3bcd] JLLWrappers v1.7.0
  [2ab3a3ac] LogExpFunctions v0.3.29
  [2fda8390] LsqFit v0.15.1
  [1914dd2f] MacroTools v0.5.16
  [e1d29d7a] Missings v1.2.0
  [d41bc354] NLSolversBase v7.10.0
  [77ba4419] NaNMath v1.1.3
  [dd2c4c9e] NearestNeighborDescent v0.3.7
  [bac558e1] OrderedCollections v1.8.1
  [90014a1f] PDMats v0.11.35
  [aea7be01] PrecompileTools v1.3.2
  [21216c6a] Preferences v1.4.3
  [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
  [efcf1570] Setfield v1.1.2
  [699a6c99] SimpleTraits v0.9.4
  [a2af1166] SortingAlgorithms v1.2.1
  [276daf66] SpecialFunctions v2.5.1
  [90137ffa] StaticArrays v1.9.13
  [1e83bf80] StaticArraysCore v1.4.3
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.7.1
  [2913bbd2] StatsBase v0.34.5
  [4c63d2b9] StatsFuns v1.5.0
  [c4f8c510] UMAP v0.1.11
⌅ [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 v1.6.0
  [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 v1.12.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [a63ad114] Mmap v1.11.0
  [ca575930] NetworkOptions v1.3.0
  [44cfe95a] Pkg v1.13.0
  [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 v1.12.0
  [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 v8.11.1+1
  [e37daf67] LibGit2_jll v1.9.0+0
  [29816b5a] LibSSH2_jll v1.11.3+1
  [14a3606d] MozillaCACerts_jll v2025.5.20
  [4536629a] OpenBLAS_jll v0.3.29+0
  [05823500] OpenLibm_jll v0.8.5+0
  [458c3c95] OpenSSL_jll v3.5.1+0
  [bea87d4a] SuiteSparse_jll v7.8.3+2
  [83775a58] Zlib_jll v1.3.1+2
  [8e850b90] libblastrampoline_jll v5.13.1+0
  [8e850ede] nghttp2_jll v1.64.0+1
  [3f19e933] p7zip_jll v17.5.0+2
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading.
     Testing Running tests...
┌ Warning: `pairwise!(r::AbstractMatrix, dist::PreMetric, a::AbstractMatrix; dims::Union{Nothing, Integer} = nothing)` is deprecated, use `pairwise!(dist, r, a; dims = dims)` instead.
│   caller = knn_search at utils.jl:63 [inlined]
└ @ Core ~/.julia/packages/UMAP/KjtQ5/src/utils.jl:63
┌ Warning: `pairwise!(r::AbstractMatrix, dist::PreMetric, a::AbstractMatrix; dims::Union{Nothing, Integer} = nothing)` is deprecated, use `pairwise!(dist, r, a; dims = dims)` instead.
│   caller = knn_search(X::Matrix{Float64}, k::Int64, metric::Euclidean, ::Val{:pairwise}) at utils.jl:63
└ @ Core ~/.julia/packages/UMAP/KjtQ5/src/utils.jl:63
Test Summary: | Pass  Total   Time
utils tests   |    9      9  20.6s
┌ Warning: `pairwise!(r::AbstractMatrix, dist::PreMetric, a::AbstractMatrix; dims::Union{Nothing, Integer} = nothing)` is deprecated, use `pairwise!(dist, r, a; dims = dims)` instead.
│   caller = knn_search at utils.jl:63 [inlined]
└ @ Core ~/.julia/packages/UMAP/KjtQ5/src/utils.jl:63
smooth_knn_dists: Test Failed at /home/pkgeval/.julia/packages/UMAP/KjtQ5/test/umap_tests.jl:57
  Expression: psum(dists, rho, sigma) - log2(k) * bandwidth < SMOOTH_K_TOLERANCE
   Evaluated: 3.415037499278844 < 1.0e-5

Stacktrace:
 [1] top-level scope
   @ ~/.julia/packages/UMAP/KjtQ5/test/umap_tests.jl:4
 [2] macro expansion
   @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined]
 [3] macro expansion
   @ ~/.julia/packages/UMAP/KjtQ5/test/umap_tests.jl:49 [inlined]
 [4] macro expansion
   @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined]
 [5] macro expansion
   @ ~/.julia/packages/UMAP/KjtQ5/test/umap_tests.jl:57 [inlined]
 [6] macro expansion
   @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:680 [inlined]
smooth_knn_dists: Test Failed at /home/pkgeval/.julia/packages/UMAP/KjtQ5/test/umap_tests.jl:68
  Expression: all(diffs .< SMOOTH_K_TOLERANCE)

Stacktrace:
 [1] top-level scope
   @ ~/.julia/packages/UMAP/KjtQ5/test/umap_tests.jl:4
 [2] macro expansion
   @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined]
 [3] macro expansion
   @ ~/.julia/packages/UMAP/KjtQ5/test/umap_tests.jl:49 [inlined]
 [4] macro expansion
   @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined]
 [5] macro expansion
   @ ~/.julia/packages/UMAP/KjtQ5/test/umap_tests.jl:68 [inlined]
 [6] macro expansion
   @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:680 [inlined]
┌ Info: Arpack.XYAUPD_Exception(1)
└ Error encountered in spectral_layout; defaulting to random layout
┌ Info: Arpack.XYAUPD_Exception(1)
└ Error encountered in spectral_layout; defaulting to random layout
Test Summary:                  | Pass  Fail  Total     Time
umap tests                     |   69     2     71  2m15.6s
  constructor                  |    4            4    41.8s
  input type stability tests   |    5            5    34.8s
  fuzzy_simpl_set              |    7            7    15.1s
  smooth_knn_dists             |    3     2      5     8.2s
  compute_membership_strengths |    3            3     0.0s
  optimize_embedding           |   23           23     4.2s
  spectral_layout              |    2            2    10.3s
  initialize_embedding         |   12           12     9.3s
  umap transform               |   10           10    12.0s
RNG of the outermost testset: Xoshiro(0x3577e7e7dcae823b, 0xd38df2e1f434e4b8, 0xaf6b9f16d04c2635, 0x4036b4cadd966959, 0xdebacd8bd9e6d0db)
ERROR: LoadError: Some tests did not pass: 69 passed, 2 failed, 0 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/UMAP/KjtQ5/test/umap_tests.jl:2
in expression starting at /home/pkgeval/.julia/packages/UMAP/KjtQ5/test/runtests.jl:11

Testing failed after 178.53s

ERROR: LoadError: Package UMAP 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:2458
  [3] test
    @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2313 [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:511
  [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:164
  [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:152
  [7] test
    @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 [inlined]
  [8] #test#81
    @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:151 [inlined]
  [9] top-level scope
    @ /PkgEval.jl/scripts/evaluate.jl:219
 [10] include(mod::Module, _path::String)
    @ Base ./Base.jl:305
 [11] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:321
 [12] _start()
    @ Base ./client.jl:554
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

PkgEval failed after 334.31s: package has test failures