Package evaluation to test SiCell on Julia 1.14.0-DEV.2802 (918269a29b*) started at 2026-08-28T08:11:12.304


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

Installing PkgEval dependencies (TestEnv)...
  Activating project at `~/.julia/environments/v1.14`

Set-up completed after 15.06s


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

Installing SiCell...
   Resolving package versions...
    Updating `~/.julia/environments/v1.14/Project.toml`
  [95f86b30] + SiCell v0.1.1
    Updating `~/.julia/environments/v1.14/Manifest.toml`
  [47edcb42] + ADTypes v1.24.0
  [621f4979] + AbstractFFTs v1.5.0
  [1520ce14] + AbstractTrees v0.4.5
  [7d9f7c33] + Accessors v0.1.45
  [79e6a3ab] + Adapt v4.7.0
  [66dad0bd] + AliasTables v1.1.3
  [ec485272] + ArnoldiMethod v0.4.0
  [7d9fca2a] + Arpack v0.5.4
  [4fba245c] + ArrayInterface v7.30.0
  [13072b0f] + AxisAlgorithms v1.1.0
  [336ed68f] + CSV v0.10.17
  [d360d2e6] + ChainRulesCore v1.26.1
  [aaaa29a8] + Clustering v0.15.8
  [944b1d66] + CodecZlib v0.7.9
  [35d6a980] + ColorSchemes v3.31.0
  [3da002f7] + ColorTypes v0.12.1
  [c3611d14] + ColorVectorSpace v0.11.0
  [5ae59095] + Colors v0.13.1
  [861a8166] + Combinatorics v1.1.0
  [38540f10] + CommonSolve v0.2.14
  [bbf7d656] + CommonSubexpressions v0.3.1
  [34da2185] + Compat v4.18.1
  [a33af91c] + CompositionsBase v0.1.2
  [187b0558] + ConstructionBase v1.6.0
  [d38c429a] + Contour v0.6.3
  [a8cc5b0e] + Crayons v4.2.0
  [9a962f9c] + DataAPI v1.16.0
  [a93c6f00] + DataFrames v1.8.2
  [864edb3b] + DataStructures v0.19.6
  [e2d170a0] + DataValueInterfaces v1.0.0
  [8bb1440f] + DelimitedFiles v1.9.1
  [163ba53b] + DiffResults v1.1.0
  [b552c78f] + DiffRules v1.16.0
  [a0c0ee7d] + DifferentiationInterface v0.7.21
  [b4f34e82] + Distances v0.10.12
  [31c24e10] + Distributions v0.25.131
  [ffbed154] + DocStringExtensions v0.9.5
  [c87230d0] + FFMPEG v0.4.5
  [b86e33f2] + FFTA v0.3.1
  [48062228] + FilePathsBase v0.9.24
  [1a297f60] + FillArrays v1.17.0
  [6a86dc24] + FiniteDiff v2.33.0
⌅ [53c48c17] + FixedPointNumbers v0.8.6
  [1fa38f19] + Format v1.3.7
  [f6369f11] + ForwardDiff v1.4.5
  [38e38edf] + GLM v1.9.5
  [28b8d3ca] + GR v0.73.27
⌅ [92fee26a] + GZip v0.6.2
  [a0844989] + Gamma v1.2.0
  [86223c79] + Graphs v1.14.0
  [42e2da0e] + Grisu v1.0.2
  [f67ccb44] + HDF5 v0.17.3
  [34004b35] + HypergeometricFunctions v0.3.30
  [09f84164] + HypothesisTests v0.11.8
  [d25df0c9] + Inflate v0.1.5
  [842dd82b] + InlineStrings v1.4.5
  [18e54dd8] + IntegerMathUtils v0.1.4
  [a98d9a8b] + Interpolations v0.16.3
  [3587e190] + InverseFunctions v0.1.17
  [41ab1584] + InvertedIndices v1.3.1
  [92d709cd] + IrrationalConstants v0.2.6
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [1019f520] + JLFzf v0.1.11
  [692b3bcd] + JLLWrappers v1.8.0
  [682c06a0] + JSON v1.7.1
  [5ab0869b] + KernelDensity v0.6.12
  [0b1a1467] + KrylovKit v0.10.4
  [b964fa9f] + LaTeXStrings v1.4.1
  [23fbe1c1] + Latexify v0.16.12
  [2ab3a3ac] + LogExpFunctions v1.0.1
⌅ [2fda8390] + LsqFit v0.15.1
  [3da0fdf6] + MPIPreferences v0.1.12
  [1914dd2f] + MacroTools v0.5.16
  [4d4711f2] + MatrixMarket v0.5.2
  [442fdcdd] + Measures v0.3.3
  [e1d29d7a] + Missings v1.2.0
  [46d2c3a1] + MuladdMacro v0.2.7
  [f8716d33] + MultipleTesting v0.6.0
  [6f286f6a] + MultivariateStats v0.10.5
⌅ [d41bc354] + NLSolversBase v7.10.0
  [77ba4419] + NaNMath v1.1.4
⌅ [dd2c4c9e] + NearestNeighborDescent v0.3.8
  [b8a86587] + NearestNeighbors v0.4.29
  [510215fc] + Observables v0.5.5
  [6fe1bfb0] + OffsetArrays v1.17.0
  [bac558e1] + OrderedCollections v2.0.1
  [90014a1f] + PDMats v0.11.41
  [65ce6f38] + PackageExtensionCompat v1.0.2
⌅ [69de0a69] + Parsers v2.8.7
  [ccf2f8ad] + PlotThemes v3.3.0
  [995b91a9] + PlotUtils v1.4.4
  [91a5bcdd] + Plots v1.41.7
  [2dfb63ee] + PooledArrays v1.4.3
  [aea7be01] + PrecompileTools v1.3.4
  [21216c6a] + Preferences v1.5.2
  [08abe8d2] + PrettyTables v3.4.8
  [27ebfcd6] + Primes v0.5.7
  [43287f4e] + PtrArrays v1.4.0
  [1fd47b50] + QuadGK v2.11.3
  [c84ed2f1] + Ratios v0.4.5
  [3cdcf5f2] + RecipesBase v1.3.4
  [01d81517] + RecipesPipeline v0.6.12
  [189a3867] + Reexport v1.2.2
  [05181044] + RelocatableFolders v1.0.1
  [ae029012] + Requires v1.3.1
  [79098fc4] + Rmath v0.9.0
  [f2b01f46] + Roots v3.0.7
  [6c6a2e73] + Scratch v1.3.0
  [91c51154] + SentinelArrays v1.4.10
  [efcf1570] + Setfield v1.1.2
  [1277b4bf] + ShiftedArrays v2.0.0
  [992d4aef] + Showoff v1.0.3
  [95f86b30] + SiCell v0.1.1
  [699a6c99] + SimpleTraits v0.9.6
  [47aef6b3] + SimpleWeightedGraphs v1.5.1
  [a2af1166] + SortingAlgorithms v1.2.3
  [276daf66] + SpecialFunctions v2.9.0
  [860ef19b] + StableRNGs v1.0.4
  [90137ffa] + StaticArrays v1.9.19
  [1e83bf80] + StaticArraysCore v1.4.4
  [10745b16] + Statistics v1.11.1
  [82ae8749] + StatsAPI v1.8.0
  [2913bbd2] + StatsBase v0.34.13
  [4c63d2b9] + StatsFuns v2.2.1
  [3eaba693] + StatsModels v0.7.10
  [f3b207a7] + StatsPlots v0.15.8
  [892a3eda] + StringManipulation v0.5.0
  [ec057cc2] + StructUtils v2.8.5
  [ab02a1b2] + TableOperations v1.2.0
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.14.0
  [62fd8b95] + TensorCore v0.1.1
  [3bb67fe8] + TranscodingStreams v0.11.3
⌅ [c4f8c510] + UMAP v0.1.11
  [1cfade01] + UnicodeFun v0.4.1
  [41fe7b60] + Unzip v0.2.0
  [409d34a3] + VectorInterface v0.6.0
  [ea10d353] + WeakRefStrings v1.4.3
  [cc8bc4a8] + Widgets v0.6.8
  [efce3f68] + WoodburyMatrices v1.1.0
  [76eceee3] + WorkerUtilities v1.6.1
⌅ [68821587] + Arpack_jll v3.5.2+0
  [6e34b625] + Bzip2_jll v1.0.9+0
  [83423d85] + Cairo_jll v1.18.7+0
  [ee1fde0b] + Dbus_jll v1.16.2+0
  [2702e6a9] + EpollShim_jll v0.0.20230411+1
  [2e619515] + Expat_jll v2.8.3+0
⌅ [b22a6f82] + FFMPEG_jll v8.1.2+0
  [a3f928ae] + Fontconfig_jll v2.17.1+0
  [d7e528f0] + FreeType2_jll v2.14.3+1
  [559328eb] + FriBidi_jll v1.0.17+0
  [0656b61e] + GLFW_jll v3.5.1+0
  [d2c73de3] + GR_jll v0.73.27+0
⌅ [b0724c58] + GettextRuntime_jll v0.22.4+0
  [61579ee1] + Ghostscript_jll v9.55.1+0
  [7746bdde] + Glib_jll v2.88.3+0
  [3b182d85] + Graphite2_jll v1.3.16+0
⌅ [0234f1f7] + HDF5_jll v2.1.2+0
⌅ [2e76f6c2] + HarfBuzz_jll v8.5.1+0
  [e33a78d0] + Hwloc_jll v2.14.0+0
  [aacddb02] + JpegTurbo_jll v3.2.0+1
  [c1c5ebd0] + LAME_jll v3.100.3+0
  [88015f11] + LERC_jll v4.1.0+0
  [1d63c593] + LLVMOpenMP_jll v22.1.7+0
⌅ [e9f186c6] + Libffi_jll v3.4.7+0
  [7e76a0d4] + Libglvnd_jll v1.7.1+1
  [94ce4f54] + Libiconv_jll v1.18.0+0
  [4b2f31a3] + Libmount_jll v2.42.0+0
  [89763e89] + Libtiff_jll v4.7.3+0
  [38a345b3] + Libuuid_jll v2.42.0+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
  [e7412a2a] + Ogg_jll v1.3.6+0
  [fe0851c0] + OpenMPI_jll v5.0.11+0
  [efe28fd5] + OpenSpecFun_jll v0.5.6+0
  [91d4177d] + Opus_jll v1.6.1+0
  [36c8627f] + Pango_jll v1.58.0+0
  [30392449] + Pixman_jll v0.46.4+0
  [c0090381] + Qt6Base_jll v6.10.2+2
  [629bc702] + Qt6Declarative_jll v6.10.2+2
  [ce943373] + Qt6ShaderTools_jll v6.10.2+1
  [6de9746b] + Qt6Svg_jll v6.10.2+0
  [e99dba38] + Qt6Wayland_jll v6.10.2+1
  [f50d1b31] + Rmath_jll v0.5.2+0
  [a44049a8] + Vulkan_Loader_jll v1.3.243+0
  [a2964d1f] + Wayland_jll v1.24.0+0
⌅ [02c8fc9c] + XML2_jll v2.13.9+0
  [ffd25f8a] + XZ_jll v5.8.3+0
  [f67eecfb] + Xorg_libICE_jll v1.1.2+0
  [c834827a] + Xorg_libSM_jll v1.2.6+0
  [4f6342f7] + Xorg_libX11_jll v1.8.13+0
  [0c0b7dd1] + Xorg_libXau_jll v1.0.13+0
  [935fb764] + Xorg_libXcursor_jll v1.2.4+0
  [a3789734] + Xorg_libXdmcp_jll v1.1.6+0
  [1082639a] + Xorg_libXext_jll v1.3.8+0
  [d091e8ba] + Xorg_libXfixes_jll v6.0.2+0
  [a51aa0fd] + Xorg_libXi_jll v1.8.4+0
  [d1454406] + Xorg_libXinerama_jll v1.1.7+0
  [ec84b674] + Xorg_libXrandr_jll v1.5.6+0
  [ea2f1a96] + Xorg_libXrender_jll v0.9.12+0
  [a65dc6b1] + Xorg_libpciaccess_jll v0.19.0+0
  [c7cfdc94] + Xorg_libxcb_jll v1.17.1+0
  [cc61e674] + Xorg_libxkbfile_jll v1.2.0+0
  [e920d4aa] + Xorg_xcb_util_cursor_jll v0.1.6+0
  [12413925] + Xorg_xcb_util_image_jll v0.4.1+0
  [2def613f] + Xorg_xcb_util_jll v0.4.1+0
  [975044d2] + Xorg_xcb_util_keysyms_jll v0.4.1+0
  [0d47668e] + Xorg_xcb_util_renderutil_jll v0.3.10+0
  [c22f9ab0] + Xorg_xcb_util_wm_jll v0.4.2+0
  [35661453] + Xorg_xkbcomp_jll v1.4.7+0
  [33bec58e] + Xorg_xkeyboard_config_jll v2.47.0+2
  [c5fb5394] + Xorg_xtrans_jll v1.6.0+0
⌅ [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 v0.10.15+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
  [35ca27e7] + eudev_jll v3.2.14+0
⌅ [214eeab7] + fzf_jll v0.61.1+0
  [477f73a3] + libaec_jll v1.1.7+0
  [a4ae2306] + libaom_jll v3.14.1+0
  [0ac62f75] + libass_jll v0.17.4+0
  [1183f4f0] + libdecor_jll v0.2.2+0
  [8e53e030] + libdrm_jll v2.4.134+0
  [2db6ffa8] + libevdev_jll v1.13.4+0
  [f638f0a6] + libfdk_aac_jll v2.0.4+0
  [36db933b] + libinput_jll v1.28.1+0
  [b53b4c65] + libpng_jll v1.6.58+0
  [9a156e7d] + libva_jll v2.23.0+0
  [f27f6e37] + libvorbis_jll v1.3.8+0
⌅ [9aeb927a] + mpif_jll v0.1.7+0
  [009596ad] + mtdev_jll v1.1.7+0
  [cddc5d3d] + s2n_tls_jll v1.7.3+0
⌅ [1270edf5] + x264_jll v10164.0.1+0
  [dfaa095f] + x265_jll v4.1.0+0
  [d8fb68d0] + xkbcommon_jll v1.13.0+0
  [0dad84c5] + ArgTools v1.2.0
  [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 v1.13.0
  [4af54fe1] + LazyArtifacts v1.11.0
  [b27032c2] + LibCURL v1.0.0
  [76f85450] + LibGit2 v1.11.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.14.0
  [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
  [3fa0cd96] + REPL v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v1.13.0
  [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
  [a4e569a6] + Tar v1.10.0
  [8dfed614] + Test v1.11.0
  [cf7118a7] + UUIDs v1.11.0
  [4ec0a83e] + Unicode v1.11.0
  [e66e0078] + CompilerSupportLibraries_jll v1.5.7+0
  [deac9b47] + LibCURL_jll v8.21.0+0
  [e37daf67] + LibGit2_jll v1.9.6+0
  [29816b5a] + LibSSH2_jll v1.11.103+0
  [14a3606d] + MozillaCACerts_jll v2026.7.16
  [4536629a] + OpenBLAS_jll v0.3.34+0
  [05823500] + OpenLibm_jll v0.8.7+0
  [458c3c95] + OpenSSL_jll v3.5.7+0
  [efcefdf7] + PCRE2_jll v10.47.0+0
  [bea87d4a] + SuiteSparse_jll v7.10.1+0
  [83775a58] + Zlib_jll v1.3.2+0
  [3161d3a3] + Zstd_jll v1.5.7+1
  [8e850b90] + libblastrampoline_jll v5.15.0+0
  [8e850ede] + nghttp2_jll v1.69.0+0
  [3f19e933] + p7zip_jll v17.8.0+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 11.89s


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

Precompiling PkgEval dependencies...

Precompiling package dependencies...
Precompiling project...
  32.9 s  ✓ SiCell
  1 dependency successfully precompiled in 39 seconds. 346 already precompiled.

Precompilation completed after 74.62s


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

     Testing SiCell
      Status `/tmp/jl_aVLv4T/Project.toml`
  [7d9fca2a] Arpack v0.5.4
  [336ed68f] CSV v0.10.17
  [aaaa29a8] Clustering v0.15.8
  [a93c6f00] DataFrames v1.8.2
  [31c24e10] Distributions v0.25.131
  [38e38edf] GLM v1.9.5
⌅ [92fee26a] GZip v0.6.2
  [86223c79] Graphs v1.14.0
  [f67ccb44] HDF5 v0.17.3
  [09f84164] HypothesisTests v0.11.8
  [0b1a1467] KrylovKit v0.10.4
  [4d4711f2] MatrixMarket v0.5.2
  [f8716d33] MultipleTesting v0.6.0
  [6f286f6a] MultivariateStats v0.10.5
  [b8a86587] NearestNeighbors v0.4.29
  [91a5bcdd] Plots v1.41.7
  [95f86b30] SiCell v0.1.1
  [47aef6b3] SimpleWeightedGraphs v1.5.1
  [10745b16] Statistics v1.11.1
  [2913bbd2] StatsBase v0.34.13
  [f3b207a7] StatsPlots v0.15.8
⌅ [c4f8c510] UMAP v0.1.11
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.14.0
  [9a3f8284] Random v1.11.0
  [2f01184e] SparseArrays v1.13.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_aVLv4T/Manifest.toml`
  [47edcb42] ADTypes v1.24.0
  [621f4979] AbstractFFTs v1.5.0
  [1520ce14] AbstractTrees v0.4.5
  [7d9f7c33] Accessors v0.1.45
  [79e6a3ab] Adapt v4.7.0
  [66dad0bd] AliasTables v1.1.3
  [ec485272] ArnoldiMethod v0.4.0
  [7d9fca2a] Arpack v0.5.4
  [4fba245c] ArrayInterface v7.30.0
  [13072b0f] AxisAlgorithms v1.1.0
  [336ed68f] CSV v0.10.17
  [d360d2e6] ChainRulesCore v1.26.1
  [aaaa29a8] Clustering v0.15.8
  [944b1d66] CodecZlib v0.7.9
  [35d6a980] ColorSchemes v3.31.0
  [3da002f7] ColorTypes v0.12.1
  [c3611d14] ColorVectorSpace v0.11.0
  [5ae59095] Colors v0.13.1
  [861a8166] Combinatorics v1.1.0
  [38540f10] CommonSolve v0.2.14
  [bbf7d656] CommonSubexpressions v0.3.1
  [34da2185] Compat v4.18.1
  [a33af91c] CompositionsBase v0.1.2
  [187b0558] ConstructionBase v1.6.0
  [d38c429a] Contour v0.6.3
  [a8cc5b0e] Crayons v4.2.0
  [9a962f9c] DataAPI v1.16.0
  [a93c6f00] DataFrames v1.8.2
  [864edb3b] DataStructures v0.19.6
  [e2d170a0] DataValueInterfaces v1.0.0
  [8bb1440f] DelimitedFiles v1.9.1
  [163ba53b] DiffResults v1.1.0
  [b552c78f] DiffRules v1.16.0
  [a0c0ee7d] DifferentiationInterface v0.7.21
  [b4f34e82] Distances v0.10.12
  [31c24e10] Distributions v0.25.131
  [ffbed154] DocStringExtensions v0.9.5
  [c87230d0] FFMPEG v0.4.5
  [b86e33f2] FFTA v0.3.1
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⌅ [53c48c17] FixedPointNumbers v0.8.6
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  [38e38edf] GLM v1.9.5
  [28b8d3ca] GR v0.73.27
⌅ [92fee26a] GZip v0.6.2
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  [f67ccb44] HDF5 v0.17.3
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  [682c06a0] JSON v1.7.1
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  [b964fa9f] LaTeXStrings v1.4.1
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⌅ [2fda8390] LsqFit v0.15.1
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⌅ [d41bc354] NLSolversBase v7.10.0
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⌅ [dd2c4c9e] NearestNeighborDescent v0.3.8
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⌅ [69de0a69] Parsers v2.8.7
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  [efcf1570] Setfield v1.1.2
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  [992d4aef] Showoff v1.0.3
  [95f86b30] SiCell v0.1.1
  [699a6c99] SimpleTraits v0.9.6
  [47aef6b3] SimpleWeightedGraphs v1.5.1
  [a2af1166] SortingAlgorithms v1.2.3
  [276daf66] SpecialFunctions v2.9.0
  [860ef19b] StableRNGs v1.0.4
  [90137ffa] StaticArrays v1.9.19
  [1e83bf80] StaticArraysCore v1.4.4
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.8.0
  [2913bbd2] StatsBase v0.34.13
  [4c63d2b9] StatsFuns v2.2.1
  [3eaba693] StatsModels v0.7.10
  [f3b207a7] StatsPlots v0.15.8
  [892a3eda] StringManipulation v0.5.0
  [ec057cc2] StructUtils v2.8.5
  [ab02a1b2] TableOperations v1.2.0
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.14.0
  [62fd8b95] TensorCore v0.1.1
  [3bb67fe8] TranscodingStreams v0.11.3
⌅ [c4f8c510] UMAP v0.1.11
  [1cfade01] UnicodeFun v0.4.1
  [41fe7b60] Unzip v0.2.0
  [409d34a3] VectorInterface v0.6.0
  [ea10d353] WeakRefStrings v1.4.3
  [cc8bc4a8] Widgets v0.6.8
  [efce3f68] WoodburyMatrices v1.1.0
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⌅ [68821587] Arpack_jll v3.5.2+0
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  [ee1fde0b] Dbus_jll v1.16.2+0
  [2702e6a9] EpollShim_jll v0.0.20230411+1
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⌅ [b22a6f82] FFMPEG_jll v8.1.2+0
  [a3f928ae] Fontconfig_jll v2.17.1+0
  [d7e528f0] FreeType2_jll v2.14.3+1
  [559328eb] FriBidi_jll v1.0.17+0
  [0656b61e] GLFW_jll v3.5.1+0
  [d2c73de3] GR_jll v0.73.27+0
⌅ [b0724c58] GettextRuntime_jll v0.22.4+0
  [61579ee1] Ghostscript_jll v9.55.1+0
  [7746bdde] Glib_jll v2.88.3+0
  [3b182d85] Graphite2_jll v1.3.16+0
⌅ [0234f1f7] HDF5_jll v2.1.2+0
⌅ [2e76f6c2] HarfBuzz_jll v8.5.1+0
  [e33a78d0] Hwloc_jll v2.14.0+0
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  [c1c5ebd0] LAME_jll v3.100.3+0
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  [1d63c593] LLVMOpenMP_jll v22.1.7+0
⌅ [e9f186c6] Libffi_jll v3.4.7+0
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⌅ [b5ada748] MPIABI_jll v0.1.5+0
  [7cb0a576] MPICH_jll v5.0.1+0
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  [9237b28f] MicrosoftMPI_jll v10.1.4+3
  [e7412a2a] Ogg_jll v1.3.6+0
  [fe0851c0] OpenMPI_jll v5.0.11+0
  [efe28fd5] OpenSpecFun_jll v0.5.6+0
  [91d4177d] Opus_jll v1.6.1+0
  [36c8627f] Pango_jll v1.58.0+0
  [30392449] Pixman_jll v0.46.4+0
  [c0090381] Qt6Base_jll v6.10.2+2
  [629bc702] Qt6Declarative_jll v6.10.2+2
  [ce943373] Qt6ShaderTools_jll v6.10.2+1
  [6de9746b] Qt6Svg_jll v6.10.2+0
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  [f50d1b31] Rmath_jll v0.5.2+0
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⌅ [02c8fc9c] XML2_jll v2.13.9+0
  [ffd25f8a] XZ_jll v5.8.3+0
  [f67eecfb] Xorg_libICE_jll v1.1.2+0
  [c834827a] Xorg_libSM_jll v1.2.6+0
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  [935fb764] Xorg_libXcursor_jll v1.2.4+0
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  [d1454406] Xorg_libXinerama_jll v1.1.7+0
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  [0d47668e] Xorg_xcb_util_renderutil_jll v0.3.10+0
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  [c5fb5394] Xorg_xtrans_jll v1.6.0+0
⌅ [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 v0.10.15+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
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⌅ [214eeab7] fzf_jll v0.61.1+0
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⌅ [9aeb927a] mpif_jll v0.1.7+0
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⌅ [1270edf5] x264_jll v10164.0.1+0
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  [4607b0f0] SuiteSparse
  [fa267f1f] TOML v1.0.3
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  [bea87d4a] SuiteSparse_jll v7.10.1+0
  [83775a58] Zlib_jll v1.3.2+0
  [3161d3a3] Zstd_jll v1.5.7+1
  [8e850b90] libblastrampoline_jll v5.15.0+0
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        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...
Successfully subsetted to 3 cells.
QC Metrics calculated: avg 30.0 genes/cell.
Filtering complete: Kept 50 / 50 cells (100.0%).
Normalizing data (scale_factor=10000.0)...
Normalization complete.
Finding variable features...
Found 20 highly variable genes.
Running PCA on normalized (sparse) data...
PCA complete. Stored 5 dimensions in 'pca'.
Scaling complete for 20 features.
Running PCA on scaled (dense) data...
PCA complete. Stored 5 dimensions in 'pca_dense'.
Normalizing data (scale_factor=10000.0)...
Normalization complete.
Finding variable features...
Found 50 highly variable genes.
Running PCA on normalized (sparse) data...
PCA complete. Stored 10 dimensions in 'pca'.
Building KNN graph (k=5, dims=10)...
KNN graph built for 100 cells with 350 edges.
Running K-Means clustering (k=3)...
Clustering complete. Found 3 clusters.
Running graph clustering (method=louvain)...
Clustering complete. Found 8 clusters.
Running graph clustering (method=label_propagation)...
Clustering complete. Found 2 clusters.
Running UMAP (n_dims=2, k=15, epochs=10)...
┌ 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::LinearAlgebra.Transpose{Float64, SubArray{Float64, 2, Matrix{Float64}, Tuple{Base.Slice{Base.OneTo{Int64}}, UnitRange{Int64}}, true}}, k::Int64, metric::Distances.Euclidean, ::Val{:pairwise}) at utils.jl:63 [inlined]
└ @ UMAP ~/.julia/packages/UMAP/KjtQ5/src/utils.jl:63
UMAP complete. Stored in obj.reductions["umap"].
Merging datasets...
Found 100 common genes.
Merge complete. Total cells: 100
Normalizing data (scale_factor=10000.0)...
Normalization complete.
Finding variable features...
Found 50 highly variable genes.
Running PCA on normalized (sparse) data...
PCA complete. Stored 10 dimensions in 'pca'.
Running Harmony Integration (k=10, iter=2)...
Harmony complete. Corrected embedding stored in reductions["harmony"].
Running BBKNN graph construction...
BBKNN complete. Graph stored in obj.graphs["neighbors"].
  🔍 Mixing Score: 0.5606 (Target ≈ 0.5)
Normalizing data (scale_factor=10000.0)...
Normalization complete.
Finding variable features...
Found 50 highly variable genes.
Running PCA on normalized (sparse) data...
PCA complete. Stored 10 dimensions in 'pca'.
Building KNN graph (k=10, dims=10)...
KNN graph built for 50 cells with 339 edges.
Constructing Diffusion Map from 50 cells...
Using existing neighbor graph...
Diffusion Map complete. Components: 5
Computing DC1-based continuous pseudotime...
  Root cell 1 pseudotime: 0.2524
  Unique values: 50  (continuous = good)
  Range: 0.0 – 1.0
Pseudotime stored in meta_data['dpt'] (method=dc1).
Normalizing data (scale_factor=10000.0)...
Normalization complete.
Calculating statistics for 100 genes across 3 clusters using 1 threads...
Adjusting p-values using Benjamini-Hochberg...
Normalizing data (scale_factor=10000.0)...
Normalization complete.
Calculating statistics for 100 genes across 3 clusters using 1 threads...
Adjusting p-values using Benjamini-Hochberg...
CellMarker 2.0 loaded: 8 entries, 2 cell types, 1 species.
Calculating annotation scores for 0 clusters using 1 threads...
Annotation complete. Labels stored in 'cell_type'.
Normalizing data (scale_factor=10000.0)...
Normalization complete.
Finding variable features...
Found 50 highly variable genes.
Running PCA on normalized (sparse) data...
PCA complete. Stored 10 dimensions in 'pca'.
Running UMAP (n_dims=2, k=15, epochs=5)...
UMAP complete. Stored in obj.reductions["umap"].
Building KNN graph (k=15, dims=10)...
KNN graph built for 50 cells with 501 edges.

Cluster sizes:
Cluster 1 => 17 cells
Cluster 2 => 17 cells
Cluster 3 => 16 cells

Connectivity matrix:
3×3 Matrix{Float64}:
 0.0    1.0    0.867
 1.0    0.0    0.892
 0.867  0.892  0.0
Test Summary:                 | Pass  Total     Time
SiCell.jl Comprehensive Suite |   29     29  4m59.6s
     Testing SiCell tests passed 

Testing completed after 350.01s

PkgEval succeeded after 485.37s