Package evaluation to test SMLMDriftCorrection on Julia 1.14.0-DEV.1720 (f38c537ec6*) started at 2026-02-15T23:24:02.203 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 11.62s ################################################################################ # Installation # Installing SMLMDriftCorrection... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [34bda2d1] + SMLMDriftCorrection v0.2.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [47edcb42] + ADTypes v1.21.0 [621f4979] + AbstractFFTs v1.5.0 ⌅ [7f219486] + AbstractNFFTs v0.8.2 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.43 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [dce04be8] + ArgCheck v2.5.0 [4fba245c] + ArrayInterface v7.22.0 [13072b0f] + AxisAlgorithms v1.1.0 [198e06fe] + BangBang v0.4.8 [9718e550] + Baselet v0.1.1 [26cce99e] + BasicInterpolators v0.7.1 [e1450e63] + BufferedStreams v1.2.2 [d360d2e6] + ChainRulesCore v1.26.0 [944b1d66] + CodecZlib v0.7.8 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [6add18c4] + ContextVariablesX v0.1.3 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 [244e2a9f] + DefineSingletons v0.1.2 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [a0c0ee7d] + DifferentiationInterface v0.7.16 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.123 [ffbed154] + DocStringExtensions v0.9.5 [4e289a0a] + EnumX v1.0.6 [7a1cc6ca] + FFTW v1.10.0 [cc61a311] + FLoops v0.2.2 [b9860ae5] + FLoopsBase v0.1.1 [5789e2e9] + FileIO v1.18.0 [1a297f60] + FillArrays v1.16.0 [6a86dc24] + FiniteDiff v2.29.0 [f6369f11] + ForwardDiff v1.3.2 [b18b359b] + FourierTools v0.4.9 [f67ccb44] + HDF5 v0.17.2 [076d061b] + HashArrayMappedTries v0.2.0 [34004b35] + HypergeometricFunctions v0.3.28 [613c443e] + IndexFunArrays v0.2.7 [22cec73e] + InitialValues v0.3.1 [a98d9a8b] + Interpolations v0.16.2 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 ⌅ [033835bb] + JLD2 v0.5.15 [692b3bcd] + JLLWrappers v1.7.1 [b14d175d] + JuliaVariables v0.2.4 [3db4a2ba] + LegendrePolynomials v0.4.5 ⌃ [d3d80556] + LineSearches v7.5.1 [2ab3a3ac] + LogExpFunctions v0.3.29 ⌅ [23992714] + MAT v0.10.7 [d8e11817] + MLStyle v0.4.17 [3da0fdf6] + MPIPreferences v0.1.11 [1914dd2f] + MacroTools v0.5.16 [c03570c3] + Memoize v0.4.4 [128add7d] + MicroCollections v0.2.0 [de9ac726] + MicroscopePSFs v0.5.4 [e1d29d7a] + Missings v1.2.0 [d3d30c82] + MutableShiftedArrays v0.3.1 [98581153] + NDTools v0.8.1 ⌅ [efe261a4] + NFFT v0.13.7 ⌅ [d41bc354] + NLSolversBase v7.10.0 [77ba4419] + NaNMath v1.1.3 [71a1bf82] + NameResolution v0.1.5 [b8a86587] + NearestNeighbors v0.4.27 [6fe1bfb0] + OffsetArrays v1.17.0 ⌅ [429524aa] + Optim v1.13.3 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.37 [5432bcbf] + PaddedViews v0.5.12 [85a6dd25] + PositiveFactorizations v0.2.4 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 [8162dcfd] + PrettyPrint v0.2.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [c84ed2f1] + Ratios v0.4.5 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [5488f106] + SMLMData v0.7.0 [34bda2d1] + SMLMDriftCorrection v0.2.0 [5a0a87e4] + SMLMSim v0.7.0 [7e506255] + ScopedValues v1.5.0 [efcf1570] + Setfield v1.1.2 [1277b4bf] + ShiftedArrays v2.0.0 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.7.1 [171d559e] + SplittablesBase v0.1.15 [90137ffa] + StaticArrays v1.9.16 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [4c63d2b9] + StatsFuns v1.5.2 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [3bb67fe8] + TranscodingStreams v0.11.3 [28d57a85] + Transducers v0.4.85 [efce3f68] + WoodburyMatrices v1.1.0 [f5851436] + FFTW_jll v3.3.11+0 ⌅ [0234f1f7] + HDF5_jll v1.14.6+0 [e33a78d0] + Hwloc_jll v2.12.2+0 [1d5cc7b8] + IntelOpenMP_jll v2025.2.0+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [856f044c] + MKL_jll v2025.2.0+0 ⌅ [7cb0a576] + MPICH_jll v4.3.2+0 [f1f71cc9] + MPItrampoline_jll v5.5.4+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [fe0851c0] + OpenMPI_jll v5.0.9+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 ⌅ [02c8fc9c] + XML2_jll v2.13.9+0 [a65dc6b1] + Xorg_libpciaccess_jll v0.18.1+0 [477f73a3] + libaec_jll v1.1.5+0 [1317d2d5] + oneTBB_jll v2022.0.0+1 [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 v1.13.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [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 [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 v8.18.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.30+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.5+0 [efcefdf7] + PCRE2_jll v10.47.0+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 v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+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 11.09s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 10830.2 ms ✓ SMLMSim 14129.8 ms ✓ SMLMDriftCorrection 2 dependencies successfully precompiled in 28 seconds. 208 already precompiled. Precompilation completed after 53.9s ################################################################################ # Testing # Testing SMLMDriftCorrection Status `/tmp/jl_qhF7eS/Project.toml` [34bda2d1] SMLMDriftCorrection v0.2.0 [5a0a87e4] SMLMSim v0.7.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_qhF7eS/Manifest.toml` [47edcb42] ADTypes v1.21.0 [621f4979] AbstractFFTs v1.5.0 ⌅ [7f219486] AbstractNFFTs v0.8.2 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.43 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [dce04be8] ArgCheck v2.5.0 [4fba245c] ArrayInterface v7.22.0 [13072b0f] AxisAlgorithms v1.1.0 [198e06fe] BangBang v0.4.8 [9718e550] Baselet v0.1.1 [26cce99e] BasicInterpolators v0.7.1 [e1450e63] BufferedStreams v1.2.2 [d360d2e6] ChainRulesCore v1.26.0 [944b1d66] CodecZlib v0.7.8 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [6add18c4] ContextVariablesX v0.1.3 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [244e2a9f] DefineSingletons v0.1.2 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [a0c0ee7d] DifferentiationInterface v0.7.16 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [4e289a0a] EnumX v1.0.6 [7a1cc6ca] FFTW v1.10.0 [cc61a311] FLoops v0.2.2 [b9860ae5] FLoopsBase v0.1.1 [5789e2e9] FileIO v1.18.0 [1a297f60] FillArrays v1.16.0 [6a86dc24] FiniteDiff v2.29.0 [f6369f11] ForwardDiff v1.3.2 [b18b359b] FourierTools v0.4.9 [f67ccb44] HDF5 v0.17.2 [076d061b] HashArrayMappedTries v0.2.0 [34004b35] HypergeometricFunctions v0.3.28 [613c443e] IndexFunArrays v0.2.7 [22cec73e] InitialValues v0.3.1 [a98d9a8b] Interpolations v0.16.2 [3587e190] InverseFunctions v0.1.17 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 ⌅ [033835bb] JLD2 v0.5.15 [692b3bcd] JLLWrappers v1.7.1 [b14d175d] JuliaVariables v0.2.4 [3db4a2ba] LegendrePolynomials v0.4.5 ⌃ [d3d80556] LineSearches v7.5.1 [2ab3a3ac] LogExpFunctions v0.3.29 ⌅ [23992714] MAT v0.10.7 [d8e11817] MLStyle v0.4.17 [3da0fdf6] MPIPreferences v0.1.11 [1914dd2f] MacroTools v0.5.16 [c03570c3] Memoize v0.4.4 [128add7d] MicroCollections v0.2.0 [de9ac726] MicroscopePSFs v0.5.4 [e1d29d7a] Missings v1.2.0 [d3d30c82] MutableShiftedArrays v0.3.1 [98581153] NDTools v0.8.1 ⌅ [efe261a4] NFFT v0.13.7 ⌅ [d41bc354] NLSolversBase v7.10.0 [77ba4419] NaNMath v1.1.3 [71a1bf82] NameResolution v0.1.5 [b8a86587] NearestNeighbors v0.4.27 [6fe1bfb0] OffsetArrays v1.17.0 ⌅ [429524aa] Optim v1.13.3 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 [5432bcbf] PaddedViews v0.5.12 [85a6dd25] PositiveFactorizations v0.2.4 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.1 [8162dcfd] PrettyPrint v0.2.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [c84ed2f1] Ratios v0.4.5 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [5488f106] SMLMData v0.7.0 [34bda2d1] SMLMDriftCorrection v0.2.0 [5a0a87e4] SMLMSim v0.7.0 [7e506255] ScopedValues v1.5.0 [efcf1570] Setfield v1.1.2 [1277b4bf] ShiftedArrays v2.0.0 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.7.1 [171d559e] SplittablesBase v0.1.15 [90137ffa] StaticArrays v1.9.16 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [28d57a85] Transducers v0.4.85 [efce3f68] WoodburyMatrices v1.1.0 [f5851436] FFTW_jll v3.3.11+0 ⌅ [0234f1f7] HDF5_jll v1.14.6+0 [e33a78d0] Hwloc_jll v2.12.2+0 [1d5cc7b8] IntelOpenMP_jll v2025.2.0+0 [94ce4f54] Libiconv_jll v1.18.0+0 [856f044c] MKL_jll v2025.2.0+0 ⌅ [7cb0a576] MPICH_jll v4.3.2+0 [f1f71cc9] MPItrampoline_jll v5.5.4+0 [9237b28f] MicrosoftMPI_jll v10.1.4+3 [fe0851c0] OpenMPI_jll v5.0.9+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 ⌅ [02c8fc9c] XML2_jll v2.13.9+0 [a65dc6b1] Xorg_libpciaccess_jll v0.18.1+0 [477f73a3] libaec_jll v1.1.5+0 [1317d2d5] oneTBB_jll v2022.0.0+1 [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 v1.13.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v1.0.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.14.0 [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 [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 v8.18.0+0 [e37daf67] LibGit2_jll v1.9.2+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.30+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.5+0 [efcefdf7] PCRE2_jll v10.47.0+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 v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+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... 2D: N = 3681, entropy_HD = -10001.434267383402, ub_entropy = -9994.569709120982 3D: N = 3757, entropy_HD = -15932.118535335281, ub_entropy = -15924.134083626375 findshift 2D identity: N = 3681 findshift 2D shift: N = 3681 findshift 3D identity: N3 = 3757 findshift 3D shift: N3 = 3757 rmsd 2D [correctdrift] = 1.2746214219931614e-16 rmsd 2D (singlepass) = 0.05874193106990441 rmsd 2D (fft) = 0.13502342153302577 [ Info: SMLMDriftCorrection: iterative mode (max_iterations=3, tol=0.001) [ Info: SMLMDriftCorrection: singlepass mode [ Info: SMLMDriftCorrection: starting intra-dataset correction [ Info: SMLMDriftCorrection: inter-dataset alignment (vs DS1) [ Info: SMLMDriftCorrection: refining inter-dataset alignment (vs earlier) [ Info: SMLMDriftCorrection: initial entropy = -9993.728936552263 [ Info: SMLMDriftCorrection: iteration 2, entropy=-9994.023289519093, max_shift_change=0.04959519444171146 [ Info: SMLMDriftCorrection: iteration 3, entropy=-9993.686790779642, max_shift_change=0.048640039759878274 rmsd 2D (iterative) = 0.10583067277100514 Warm start: entropy -9993.728936552263 -> -9994.061188461765 Continuation: 1 -> 3 iterations [ Info: SMLMDriftCorrection: singlepass mode [ Info: SMLMDriftCorrection: starting intra-dataset correction [ Info: SMLMDriftCorrection: inter-dataset alignment (vs DS1) [ Info: SMLMDriftCorrection: refining inter-dataset alignment (vs earlier) rmsd 2D (maxn=100) = 0.05933005028406434 rmsd 2D (degree=3) = 0.06294614495233745 rmsd 3D [correctdrift] = 1.0989828397614332e-16 rmsd 3D (default) = 0.014720524062400691 [ Info: SMLMDriftCorrection: singlepass mode [ Info: SMLMDriftCorrection: starting intra-dataset correction [ Info: SMLMDriftCorrection: inter-dataset alignment (vs DS1) [ Info: SMLMDriftCorrection: refining inter-dataset alignment (vs earlier) rmsd 3D (maxn=100) = 0.014721963548629409 [ Info: SMLMDriftCorrection: singlepass mode [ Info: SMLMDriftCorrection: starting intra-dataset correction [ Info: SMLMDriftCorrection: inter-dataset alignment (vs DS1) [ Info: SMLMDriftCorrection: refining inter-dataset alignment (vs earlier) rmsd 2D (auto_roi=true) = 0.04923578245029468 Test Summary: | Pass Total Time SMLMDriftCorrection.jl | 64 64 14m05.9s Testing SMLMDriftCorrection tests passed Testing completed after 873.86s PkgEval succeeded after 967.28s