Package evaluation of SMLMSim on Julia 1.13.0-DEV.111 (ce76dbf07d*) started at 2025-02-28T10:22:21.244


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# Set-up
#


Set-up completed after 0.24s


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# Installation
#

Installing SMLMSim...
   Resolving package versions...
   Installed HDF5 ─ v0.16.16
    Updating `~/.julia/environments/v1.13/Project.toml`
  [5a0a87e4] + SMLMSim v0.2.1
    Updating `~/.julia/environments/v1.13/Manifest.toml`
  [621f4979] + AbstractFFTs v1.5.0
  [398f06c4] + AbstractLattices v0.3.1
  [1520ce14] + AbstractTrees v0.4.5
  [79e6a3ab] + Adapt v4.2.0
  [66dad0bd] + AliasTables v1.1.3
  [27a7e980] + Animations v0.4.2
  [ec485272] + ArnoldiMethod v0.4.0
  [4fba245c] + ArrayInterface v7.18.0
  [67c07d97] + Automa v1.1.0
⌃ [13072b0f] + AxisAlgorithms v1.0.1
  [39de3d68] + AxisArrays v0.4.7
  [62783981] + BitTwiddlingConvenienceFunctions v0.1.6
  [e1450e63] + BufferedStreams v1.2.2
  [fa961155] + CEnum v0.5.0
  [2a0fbf3d] + CPUSummary v0.2.6
  [336ed68f] + CSV v0.10.15
  [159f3aea] + Cairo v1.1.1
⌅ [13f3f980] + CairoMakie v0.11.9
  [aafaddc9] + CatIndices v0.2.2
  [d360d2e6] + ChainRulesCore v1.25.1
  [fb6a15b2] + CloseOpenIntervals v0.1.13
  [aaaa29a8] + Clustering v0.15.8
  [944b1d66] + CodecZlib v0.7.8
  [a2cac450] + ColorBrewer v0.4.1
⌃ [35d6a980] + ColorSchemes v3.26.0
⌅ [3da002f7] + ColorTypes v0.11.5
⌅ [c3611d14] + ColorVectorSpace v0.9.10
⌅ [5ae59095] + Colors v0.12.11
  [861a8166] + Combinatorics v1.0.2
  [bbf7d656] + CommonSubexpressions v0.3.1
  [f70d9fcc] + CommonWorldInvalidations v1.0.0
  [34da2185] + Compat v4.16.0
  [ed09eef8] + ComputationalResources v0.3.2
  [187b0558] + ConstructionBase v1.5.8
  [d38c429a] + Contour v0.6.3
  [150eb455] + CoordinateTransformations v0.6.4
  [adafc99b] + CpuId v0.3.1
  [a8cc5b0e] + Crayons v4.1.1
  [dc8bdbbb] + CustomUnitRanges v1.0.2
  [9a962f9c] + DataAPI v1.16.0
  [a93c6f00] + DataFrames v1.7.0
  [864edb3b] + DataStructures v0.18.20
  [e2d170a0] + DataValueInterfaces v1.0.0
⌅ [927a84f5] + DelaunayTriangulation v0.8.12
  [163ba53b] + DiffResults v1.1.0
  [b552c78f] + DiffRules v1.15.1
  [b4f34e82] + Distances v0.10.12
  [31c24e10] + Distributions v0.25.117
  [ffbed154] + DocStringExtensions v0.9.3
  [4e289a0a] + EnumX v1.0.4
  [429591f6] + ExactPredicates v2.2.8
  [411431e0] + Extents v0.1.5
  [4f61f5a4] + FFTViews v0.3.2
  [7a1cc6ca] + FFTW v1.8.1
  [5789e2e9] + FileIO v1.17.0
  [8fc22ac5] + FilePaths v0.8.3
  [48062228] + FilePathsBase v0.9.23
  [1a297f60] + FillArrays v1.13.0
  [6a86dc24] + FiniteDiff v2.27.0
  [53c48c17] + FixedPointNumbers v0.8.5
  [1fa38f19] + Format v1.3.7
  [f6369f11] + ForwardDiff v0.10.38
  [b38be410] + FreeType v4.1.1
  [663a7486] + FreeTypeAbstraction v0.10.6
  [68eda718] + GeoFormatTypes v0.4.4
  [cf35fbd7] + GeoInterface v1.4.1
⌅ [5c1252a2] + GeometryBasics v0.4.11
  [a2bd30eb] + Graphics v1.1.3
  [86223c79] + Graphs v1.12.0
⌅ [3955a311] + GridLayoutBase v0.10.2
  [42e2da0e] + Grisu v1.0.2
⌅ [f67ccb44] + HDF5 v0.16.16
  [2c695a8d] + HistogramThresholding v0.3.1
  [3e5b6fbb] + HostCPUFeatures v0.1.17
  [34004b35] + HypergeometricFunctions v0.3.27
  [615f187c] + IfElse v0.1.1
⌃ [2803e5a7] + ImageAxes v0.6.11
⌃ [c817782e] + ImageBase v0.1.5
  [cbc4b850] + ImageBinarization v0.3.1
  [f332f351] + ImageContrastAdjustment v0.3.12
⌅ [a09fc81d] + ImageCore v0.9.4
  [89d5987c] + ImageCorners v0.1.3
  [51556ac3] + ImageDistances v0.2.17
⌃ [6a3955dd] + ImageFiltering v0.7.6
⌃ [82e4d734] + ImageIO v0.6.8
⌃ [6218d12a] + ImageMagick v1.2.1
⌃ [bc367c6b] + ImageMetadata v0.9.9
  [787d08f9] + ImageMorphology v0.4.5
  [2996bd0c] + ImageQualityIndexes v0.3.7
⌃ [80713f31] + ImageSegmentation v1.8.1
  [4e3cecfd] + ImageShow v0.3.8
  [02fcd773] + ImageTransformations v0.10.1
⌃ [916415d5] + Images v0.26.1
  [9b13fd28] + IndirectArrays v1.0.0
  [d25df0c9] + Inflate v0.1.5
  [842dd82b] + InlineStrings v1.4.3
  [18e54dd8] + IntegerMathUtils v0.1.2
  [1d092043] + IntegralArrays v0.1.6
⌅ [a98d9a8b] + Interpolations v0.14.0
  [d1acc4aa] + IntervalArithmetic v0.22.23
  [8197267c] + IntervalSets v0.7.10
  [41ab1584] + InvertedIndices v1.3.1
  [92d709cd] + IrrationalConstants v0.2.4
  [f1662d9f] + Isoband v0.1.1
  [c8e1da08] + IterTools v1.10.0
  [82899510] + IteratorInterfaceExtensions v1.0.0
⌅ [033835bb] + JLD2 v0.4.54
  [692b3bcd] + JLLWrappers v1.7.0
  [682c06a0] + JSON v0.21.4
  [b835a17e] + JpegTurbo v0.1.5
  [5ab0869b] + KernelDensity v0.6.9
  [b964fa9f] + LaTeXStrings v1.4.0
  [10f19ff3] + LayoutPointers v0.1.17
  [8cdb02fc] + LazyModules v0.3.1
  [9c8b4983] + LightXML v0.9.1
  [d3d80556] + LineSearches v7.3.0
  [9b3f67b0] + LinearAlgebraX v0.2.10
  [2ab3a3ac] + LogExpFunctions v0.3.29
  [bdcacae8] + LoopVectorization v0.12.171
  [23992714] + MAT v0.10.7
  [3da0fdf6] + MPIPreferences v0.1.11
  [1914dd2f] + MacroTools v0.5.15
⌅ [ee78f7c6] + Makie v0.20.8
⌅ [20f20a25] + MakieCore v0.7.3
  [d125e4d3] + ManualMemory v0.1.8
  [dbb5928d] + MappedArrays v0.4.2
⌅ [0a4f8689] + MathTeXEngine v0.5.7
⌅ [626554b9] + MetaGraphs v0.7.2
  [de9ac726] + MicroscopePSFs v0.4.0
  [e1d29d7a] + Missings v1.2.0
  [7475f97c] + Mods v2.2.6
  [e94cdb99] + MosaicViews v0.3.4
  [3b2b4ff1] + Multisets v0.4.5
  [d41bc354] + NLSolversBase v7.8.3
  [77ba4419] + NaNMath v1.1.2
  [b8a86587] + NearestNeighbors v0.4.21
  [f09324ee] + Netpbm v1.1.1
  [510215fc] + Observables v0.5.5
  [6fe1bfb0] + OffsetArrays v1.15.0
  [52e1d378] + OpenEXR v0.3.3
  [429524aa] + Optim v1.11.0
  [bac558e1] + OrderedCollections v1.8.0
  [90014a1f] + PDMats v0.11.32
  [f57f5aa1] + PNGFiles v0.4.4
  [19eb6ba3] + Packing v0.5.1
  [5432bcbf] + PaddedViews v0.5.12
  [d96e819e] + Parameters v0.12.3
  [69de0a69] + Parsers v2.8.1
  [2ae35dd2] + Permutations v0.4.23
  [3bbf5609] + PikaParser v0.6.1
  [eebad327] + PkgVersion v0.3.3
  [995b91a9] + PlotUtils v1.4.3
  [1d0040c9] + PolyesterWeave v0.2.2
  [647866c9] + PolygonOps v0.1.2
  [f27b6e38] + Polynomials v4.0.17
  [2dfb63ee] + PooledArrays v1.4.3
  [85a6dd25] + PositiveFactorizations v0.2.4
  [aea7be01] + PrecompileTools v1.2.1
  [21216c6a] + Preferences v1.4.3
  [08abe8d2] + PrettyTables v2.4.0
  [27ebfcd6] + Primes v0.5.6
  [92933f4c] + ProgressMeter v1.10.2
  [43287f4e] + PtrArrays v1.3.0
  [4b34888f] + QOI v1.0.1
  [1fd47b50] + QuadGK v2.11.2
  [94ee1d12] + Quaternions v0.7.6
  [b3c3ace0] + RangeArrays v0.3.2
  [c84ed2f1] + Ratios v0.4.5
  [c1ae055f] + RealDot v0.1.0
  [3cdcf5f2] + RecipesBase v1.3.4
  [189a3867] + Reexport v1.2.2
  [dee08c22] + RegionTrees v0.3.2
  [05181044] + RelocatableFolders v1.0.1
  [ae029012] + Requires v1.3.1
  [286e9d63] + RingLists v0.2.9
  [79098fc4] + Rmath v0.8.0
  [6038ab10] + Rotations v1.7.1
  [5eaf0fd0] + RoundingEmulator v0.2.1
  [fdea26ae] + SIMD v3.7.1
  [94e857df] + SIMDTypes v0.1.0
  [476501e8] + SLEEFPirates v0.6.43
⌅ [5488f106] + SMLMData v0.1.2
  [5a0a87e4] + SMLMSim v0.2.1
  [6c6a2e73] + Scratch v1.2.1
  [91c51154] + SentinelArrays v1.4.8
  [efcf1570] + Setfield v1.1.2
⌅ [65257c39] + ShaderAbstractions v0.4.1
  [992d4aef] + Showoff v1.0.3
  [73760f76] + SignedDistanceFields v0.4.0
  [55797a34] + SimpleGraphs v0.8.6
  [ec83eff0] + SimplePartitions v0.3.3
  [cc47b68c] + SimplePolynomials v0.2.18
  [a6525b86] + SimpleRandom v0.3.2
  [699a6c99] + SimpleTraits v0.9.4
  [47aef6b3] + SimpleWeightedGraphs v1.4.0
  [45858cf5] + Sixel v0.1.3
  [a2af1166] + SortingAlgorithms v1.2.1
  [276daf66] + SpecialFunctions v2.5.0
⌅ [c5dd0088] + StableHashTraits v1.3.4
  [860ef19b] + StableRNGs v1.0.2
  [cae243ae] + StackViews v0.1.1
  [aedffcd0] + Static v1.1.1
  [0d7ed370] + StaticArrayInterface v1.8.0
  [90137ffa] + StaticArrays v1.9.12
  [1e83bf80] + StaticArraysCore v1.4.3
  [10745b16] + Statistics v1.11.1
  [82ae8749] + StatsAPI v1.7.0
  [2913bbd2] + StatsBase v0.34.4
  [4c63d2b9] + StatsFuns v1.3.2
  [892a3eda] + StringManipulation v0.4.1
⌅ [09ab397b] + StructArrays v0.6.21
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  [62fd8b95] + TensorCore v0.1.1
  [8290d209] + ThreadingUtilities v0.5.2
⌅ [731e570b] + TiffImages v0.10.2
  [06e1c1a7] + TiledIteration v0.5.0
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  [ea10d353] + WeakRefStrings v1.4.2
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⌅ [c73af94c] + ImageMagick_jll v6.9.13+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. To see why use `status --outdated -m`
    Building HDF5 → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/114e20044677badbc631ee6fdc80a67920561a29/build.log`

Installation completed after 16.2s


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

Precompiling PkgEval dependencies...
No packages added to or removed from `~/.julia/environments/pkgeval/Project.toml`
No packages added to or removed from `~/.julia/environments/pkgeval/Manifest.toml`

Precompiling package dependencies...
Precompiling packages...
   7982.9 ms  ✓ FreeTypeAbstraction
  10227.9 ms  ✓ MAT
  19122.4 ms  ✓ ImageTransformations
  42270.8 ms  ✓ MicroscopePSFs
  26628.1 ms  ✓ MathTeXEngine
  27132.3 ms  ✓ ImageContrastAdjustment
 443123.5 ms  ✓ Makie
 623151.2 ms  ✓ Images
 168003.1 ms  ✓ CairoMakie
 311106.1 ms  ✓ SMLMData
 580251.0 ms  ✓ SMLMSim
  11 dependencies successfully precompiled in 2275 seconds. 380 already precompiled.
  3 dependencies had output during precompilation:
┌ Makie
│  WARNING: method definition for checkbounds at /home/pkgeval/.julia/packages/Interpolations/USkTk/src/Interpolations.jl:454 declares type variable N but does not use it.
│  WARNING: method definition for checkbounds at /home/pkgeval/.julia/packages/Interpolations/USkTk/src/Interpolations.jl:457 declares type variable N but does not use it.
│  WARNING: method definition for GriddedInterpolation at /home/pkgeval/.julia/packages/Interpolations/USkTk/src/gridded/gridded.jl:37 declares type variable pad but does not use it.
│  WARNING: method definition for GriddedInterpolation at /home/pkgeval/.julia/packages/Interpolations/USkTk/src/gridded/gridded.jl:60 declares type variable pad but does not use it.
│  WARNING: method definition for interpolate! at /home/pkgeval/.julia/packages/Interpolations/USkTk/src/deprecations.jl:30 declares type variable TWeights but does not use it.
│  ┌ Warning: `stable_hash(x; version < 4)` is not supported in Julia 1.11 or higher. Calls should not error, but *may* silently produce different hashes. `stable_hash` is intended to be used for caching, so this likely will simply reduce the number of cache hits. Upgrade to using `stable_hash(x; version=4) to avoid this warning.
│  └ @ StableHashTraits ~/.julia/packages/StableHashTraits/FV3wr/src/main_interface.jl:55
└  
┌ Images
│  WARNING: Constructor for type "Alg" was extended in `ImageFiltering` without explicit qualification or import.
│    NOTE: Assumed "Alg" refers to `Algorithm.Alg`. This behavior is deprecated and may differ in future versions.`
│    NOTE: This behavior may have differed in Julia versions prior to 1.12.
│    Hint: If you intended to create a new generic function of the same name, use `function Alg end`.
│    Hint: To silence the warning, qualify `Alg` as `Algorithm.Alg` or explicitly `import Algorithm: Alg`
│  WARNING: Constructor for type "Int16" was extended in `VectorizationBase` without explicit qualification or import.
│    NOTE: Assumed "Int16" refers to `Base.Int16`. This behavior is deprecated and may differ in future versions.`
│    NOTE: This behavior may have differed in Julia versions prior to 1.12.
│    Hint: If you intended to create a new generic function of the same name, use `function Int16 end`.
│    Hint: To silence the warning, qualify `Int16` as `Base.Int16` or explicitly `import Base: Int16`
│  WARNING: Constructor for type "Int64" was extended in `VectorizationBase` without explicit qualification or import.
│    NOTE: Assumed "Int64" refers to `Base.Int64`. This behavior is deprecated and may differ in future versions.`
│    NOTE: This behavior may have differed in Julia versions prior to 1.12.
│    Hint: If you intended to create a new generic function of the same name, use `function Int64 end`.
│    Hint: To silence the warning, qualify `Int64` as `Base.Int64` or explicitly `import Base: Int64`
│  WARNING: Constructor for type "Int32" was extended in `VectorizationBase` without explicit qualification or import.
│    NOTE: Assumed "Int32" refers to `Base.Int32`. This behavior is deprecated and may differ in future versions.`
│    NOTE: This behavior may have differed in Julia versions prior to 1.12.
│    Hint: If you intended to create a new generic function of the same name, use `function Int32 end`.
│    Hint: To silence the warning, qualify `Int32` as `Base.Int32` or explicitly `import Base: Int32`
│  WARNING: Constructor for type "UInt8" was extended in `VectorizationBase` without explicit qualification or import.
│    NOTE: Assumed "UInt8" refers to `Base.UInt8`. This behavior is deprecated and may differ in future versions.`
│    NOTE: This behavior may have differed in Julia versions prior to 1.12.
│    Hint: If you intended to create a new generic function of the same name, use `function UInt8 end`.
│    Hint: To silence the warning, qualify `UInt8` as `Base.UInt8` or explicitly `import Base: UInt8`
│  WARNING: Constructor for type "UInt16" was extended in `VectorizationBase` without explicit qualification or import.
│    NOTE: Assumed "UInt16" refers to `Base.UInt16`. This behavior is deprecated and may differ in future versions.`
│    NOTE: This behavior may have differed in Julia versions prior to 1.12.
│    Hint: If you intended to create a new generic function of the same name, use `function UInt16 end`.
│    Hint: To silence the warning, qualify `UInt16` as `Base.UInt16` or explicitly `import Base: UInt16`
│  WARNING: Constructor for type "Float32" was extended in `VectorizationBase` without explicit qualification or import.
│    NOTE: Assumed "Float32" refers to `Base.Float32`. This behavior is deprecated and may differ in future versions.`
│    NOTE: This behavior may have differed in Julia versions prior to 1.12.
│    Hint: If you intended to create a new generic function of the same name, use `function Float32 end`.
│    Hint: To silence the warning, qualify `Float32` as `Base.Float32` or explicitly `import Base: Float32`
│  WARNING: Constructor for type "UInt64" was extended in `VectorizationBase` without explicit qualification or import.
│    NOTE: Assumed "UInt64" refers to `Base.UInt64`. This behavior is deprecated and may differ in future versions.`
│    NOTE: This behavior may have differed in Julia versions prior to 1.12.
│    Hint: If you intended to create a new generic function of the same name, use `function UInt64 end`.
│    Hint: To silence the warning, qualify `UInt64` as `Base.UInt64` or explicitly `import Base: UInt64`
│  WARNING: Constructor for type "Bool" was extended in `VectorizationBase` without explicit qualification or import.
│    NOTE: Assumed "Bool" refers to `Base.Bool`. This behavior is deprecated and may differ in future versions.`
│    NOTE: This behavior may have differed in Julia versions prior to 1.12.
│    Hint: If you intended to create a new generic function of the same name, use `function Bool end`.
│    Hint: To silence the warning, qualify `Bool` as `Base.Bool` or explicitly `import Base: Bool`
│  WARNING: Constructor for type "Int8" was extended in `VectorizationBase` without explicit qualification or import.
│    NOTE: Assumed "Int8" refers to `Base.Int8`. This behavior is deprecated and may differ in future versions.`
│    NOTE: This behavior may have differed in Julia versions prior to 1.12.
│    Hint: If you intended to create a new generic function of the same name, use `function Int8 end`.
│    Hint: To silence the warning, qualify `Int8` as `Base.Int8` or explicitly `import Base: Int8`
│  WARNING: Constructor for type "Float64" was extended in `VectorizationBase` without explicit qualification or import.
│    NOTE: Assumed "Float64" refers to `Base.Float64`. This behavior is deprecated and may differ in future versions.`
│    NOTE: This behavior may have differed in Julia versions prior to 1.12.
│    Hint: If you intended to create a new generic function of the same name, use `function Float64 end`.
│    Hint: To silence the warning, qualify `Float64` as `Base.Float64` or explicitly `import Base: Float64`
│  WARNING: Constructor for type "UInt32" was extended in `VectorizationBase` without explicit qualification or import.
│    NOTE: Assumed "UInt32" refers to `Base.UInt32`. This behavior is deprecated and may differ in future versions.`
│    NOTE: This behavior may have differed in Julia versions prior to 1.12.
│    Hint: If you intended to create a new generic function of the same name, use `function UInt32 end`.
│    Hint: To silence the warning, qualify `UInt32` as `Base.UInt32` or explicitly `import Base: UInt32`
│  WARNING: Constructor for type "Float16" was extended in `VectorizationBase` without explicit qualification or import.
│    NOTE: Assumed "Float16" refers to `Base.Float16`. This behavior is deprecated and may differ in future versions.`
│    NOTE: This behavior may have differed in Julia versions prior to 1.12.
│    Hint: If you intended to create a new generic function of the same name, use `function Float16 end`.
│    Hint: To silence the warning, qualify `Float16` as `Base.Float16` or explicitly `import Base: Float16`
└  
┌ SMLMSim
│  ┌ Warning: `stable_hash(x; version < 4)` is not supported in Julia 1.11 or higher. Calls should not error, but *may* silently produce different hashes. `stable_hash` is intended to be used for caching, so this likely will simply reduce the number of cache hits. Upgrade to using `stable_hash(x; version=4) to avoid this warning.
│  └ @ StableHashTraits ~/.julia/packages/StableHashTraits/FV3wr/src/main_interface.jl:55
└  

Precompilation completed after 2271.08s


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