Package evaluation to test MriResearchTools on Julia 1.10.10 (c8be17dcfd*) started at 2026-02-02T23:14:11.952 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.10` Set-up completed after 3.85s ################################################################################ # Installation # Installing MriResearchTools... Resolving package versions... Updating `~/.julia/environments/v1.10/Project.toml` [557dad86] + MriResearchTools v3.4.0 Updating `~/.julia/environments/v1.10/Manifest.toml` [621f4979] + AbstractFFTs v1.5.0 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.22.0 [13072b0f] + AxisAlgorithms v1.1.0 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [2a0fbf3d] + CPUSummary v0.2.7 [d360d2e6] + ChainRulesCore v1.26.0 [fb6a15b2] + CloseOpenIntervals v0.1.13 [944b1d66] + CodecZlib v0.7.8 [3da002f7] + ColorTypes v0.12.1 [c3611d14] + ColorVectorSpace v0.11.0 [5ae59095] + Colors v0.13.1 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [adafc99b] + CpuId v0.3.1 [9a962f9c] + DataAPI v1.16.0 ⌅ [864edb3b] + DataStructures v0.18.22 [ffbed154] + DocStringExtensions v0.9.5 [bd0ea217] + EasyRanges v0.1.4 ⌅ [7a1cc6ca] + FFTW v1.8.1 [53c48c17] + FixedPointNumbers v0.8.5 [3e5b6fbb] + HostCPUFeatures v0.1.18 [615f187c] + IfElse v0.1.1 [a09fc81d] + ImageCore v0.10.5 ⌃ [787d08f9] + ImageMorphology v0.4.6 ⌅ [a98d9a8b] + Interpolations v0.15.1 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.7.1 [10f19ff3] + LayoutPointers v0.1.17 [085fde7c] + LocalFilters v2.1.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [bdcacae8] + LoopVectorization v0.12.173 [d125e4d3] + ManualMemory v0.1.8 [dbb5928d] + MappedArrays v0.4.3 [e1d29d7a] + Missings v1.2.0 [e94cdb99] + MosaicViews v0.3.4 [557dad86] + MriResearchTools v3.4.0 [a3a9e032] + NIfTI v0.6.1 [6fe1bfb0] + OffsetArrays v1.17.0 [bac558e1] + OrderedCollections v1.8.1 [5432bcbf] + PaddedViews v0.5.12 [1d0040c9] + PolyesterWeave v0.2.2 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.5.1 [43287f4e] + PtrArrays v1.3.0 [1ea8258b] + ROMEO v1.4.0 [c84ed2f1] + Ratios v0.4.5 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.43 [431bcebd] + SciMLPublic v1.0.1 [a2af1166] + SortingAlgorithms v1.2.2 [cae243ae] + StackViews v0.1.2 [aedffcd0] + Static v1.3.1 [0d7ed370] + StaticArrayInterface v1.8.0 [90137ffa] + StaticArrays v1.9.16 [1e83bf80] + StaticArraysCore v1.4.4 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [2e8cd123] + StructuredArrays v0.2.22 [62fd8b95] + TensorCore v0.1.1 [8290d209] + ThreadingUtilities v0.5.5 [06e1c1a7] + TiledIteration v0.5.0 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [c3b1956e] + TypeUtils v1.14.0 [3a884ed6] + UnPack v1.0.2 [3d5dd08c] + VectorizationBase v0.21.72 [efce3f68] + WoodburyMatrices v1.1.0 [f5851436] + FFTW_jll v3.3.11+0 [1d5cc7b8] + IntelOpenMP_jll v2025.2.0+0 [856f044c] + MKL_jll v2025.2.0+0 [1317d2d5] + oneTBB_jll v2022.0.0+1 [0dad84c5] + ArgTools v1.1.1 [56f22d72] + Artifacts [2a0f44e3] + Base64 [ade2ca70] + Dates [8ba89e20] + Distributed [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching [b77e0a4c] + InteractiveUtils [4af54fe1] + LazyArtifacts [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 [8f399da3] + Libdl [37e2e46d] + LinearAlgebra [56ddb016] + Logging [d6f4376e] + Markdown [a63ad114] + Mmap [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.10.0 [de0858da] + Printf [3fa0cd96] + REPL [9a3f8284] + Random [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization [1a1011a3] + SharedArrays [6462fe0b] + Sockets [2f01184e] + SparseArrays v1.10.0 [10745b16] + Statistics v1.10.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test [cf7118a7] + UUIDs [4ec0a83e] + Unicode [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.4.0+0 [e37daf67] + LibGit2_jll v1.6.4+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.1010+0 [14a3606d] + MozillaCACerts_jll v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.23+5 [bea87d4a] + SuiteSparse_jll v7.2.1+1 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.52.0+1 [3f19e933] + p7zip_jll v17.4.0+2 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 9.45s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ TestEnv ~/.julia/packages/TestEnv/h9a3r/src/julia-1.9/activate_set.jl:63 Precompiling package dependencies... Precompiling packages... 6058.6 ms ✓ Interpolations 8149.8 ms ✓ Polynomials → PolynomialsFFTWExt 1446.1 ms ✓ FFTViews 26246.2 ms ✓ LoopVectorization 5513.6 ms ✓ DSP 83337.4 ms ✓ ImageFiltering 55073.2 ms ✓ LoopVectorization → SpecialFunctionsExt 12600.1 ms ✓ ImageMorphology 40007.7 ms ✓ QSM 78814.9 ms ✓ MriResearchTools 164653.3 ms ✓ QuantitativeSusceptibilityMappingTGV 18229.1 ms ✓ MriResearchTools → PhaseBasedMaskingExt 38791.3 ms ✓ MriResearchTools → QSMExt 9365.2 ms ✓ MriResearchTools → QuantitativeSusceptibilityMappingTGVExt 14 dependencies successfully precompiled in 554 seconds. 134 already precompiled. Precompilation completed after 568.69s ################################################################################ # Testing # Testing MriResearchTools ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1829 Status `/tmp/jl_Y3m9zk/Project.toml` [6a3955dd] ImageFiltering v0.7.12 [557dad86] MriResearchTools v3.4.0 [794fc106] QSM v0.5.4 [bd393529] QuantitativeSusceptibilityMappingTGV v0.5.0 [f8b46487] TestItemRunner v1.1.4 [8dfed614] Test Status `/tmp/jl_Y3m9zk/Manifest.toml` [621f4979] AbstractFFTs v1.5.0 ⌅ [79e6a3ab] Adapt v3.7.2 [66dad0bd] AliasTables v1.1.3 ⌅ [4fba245c] ArrayInterface v6.0.25 [30b0a656] ArrayInterfaceCore v0.1.29 [015c0d05] ArrayInterfaceOffsetArrays v0.1.7 [b0d46f97] ArrayInterfaceStaticArrays v0.1.5 [dd5226c6] ArrayInterfaceStaticArraysCore v0.1.4 [a9b6321e] Atomix v1.1.2 [13072b0f] AxisAlgorithms v1.1.0 [62783981] BitTwiddlingConvenienceFunctions v0.1.6 ⌃ [2a0fbf3d] CPUSummary v0.2.6 [aafaddc9] CatIndices v0.2.2 [d360d2e6] ChainRulesCore v1.26.0 ⌃ [fb6a15b2] CloseOpenIntervals v0.1.11 [944b1d66] CodecZlib v0.7.8 [3da002f7] ColorTypes v0.12.1 [c3611d14] ColorVectorSpace v0.11.0 [5ae59095] Colors v0.13.1 [34da2185] Compat v4.18.1 [ed09eef8] ComputationalResources v0.3.2 [187b0558] ConstructionBase v1.6.0 [adafc99b] CpuId v0.3.1 [dc8bdbbb] CustomUnitRanges v1.0.2 ⌅ [717857b8] DSP v0.7.10 [9a962f9c] DataAPI v1.16.0 ⌅ [864edb3b] DataStructures v0.18.22 [ffbed154] DocStringExtensions v0.9.5 [bd0ea217] EasyRanges v0.1.4 [4f61f5a4] FFTViews v0.3.2 ⌅ [7a1cc6ca] FFTW v1.8.1 [c0e83750] FastPow v0.1.0 [53c48c17] FixedPointNumbers v0.8.5 [3e5b6fbb] HostCPUFeatures v0.1.18 [615f187c] IfElse v0.1.1 [c817782e] ImageBase v0.1.7 [a09fc81d] ImageCore v0.10.5 [6a3955dd] ImageFiltering v0.7.12 ⌃ [787d08f9] ImageMorphology v0.4.6 ⌅ [a98d9a8b] Interpolations v0.15.1 [3587e190] InverseFunctions v0.1.17 [92d709cd] IrrationalConstants v0.2.6 [c8e1da08] IterTools v1.10.0 [692b3bcd] JLLWrappers v1.7.1 [63c18a36] KernelAbstractions v0.9.39 ⌃ [10f19ff3] LayoutPointers v0.1.13 [7a12625a] LinearMaps v3.11.4 [085fde7c] LocalFilters v2.1.0 [2ab3a3ac] LogExpFunctions v0.3.29 ⌃ [bdcacae8] LoopVectorization v0.12.150 [1914dd2f] MacroTools v0.5.16 [d125e4d3] ManualMemory v0.1.8 [dbb5928d] MappedArrays v0.4.3 [e1d29d7a] Missings v1.2.0 [e94cdb99] MosaicViews v0.3.4 [557dad86] MriResearchTools v3.4.0 [a3a9e032] NIfTI v0.6.1 [6fe1bfb0] OffsetArrays v1.17.0 [bac558e1] OrderedCollections v1.8.1 [5432bcbf] PaddedViews v0.5.12 ⌃ [f517fe37] Polyester v0.7.2 [1d0040c9] PolyesterWeave v0.2.2 [f27b6e38] Polynomials v4.1.0 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.5.1 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [794fc106] QSM v0.5.4 [bd393529] QuantitativeSusceptibilityMappingTGV v0.5.0 [94ee1d12] Quaternions v0.7.7 [1ea8258b] ROMEO v1.4.0 [c84ed2f1] Ratios v0.4.5 [c1ae055f] RealDot v0.1.0 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [6038ab10] Rotations v1.7.1 [94e857df] SIMDTypes v0.1.0 [476501e8] SLEEFPirates v0.6.43 [efcf1570] Setfield v1.1.2 [66db9d55] SnoopPrecompile v1.0.3 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [cae243ae] StackViews v0.1.2 ⌅ [aedffcd0] Static v0.8.10 [90137ffa] StaticArrays v1.9.16 [1e83bf80] StaticArraysCore v1.4.4 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 ⌅ [7792a7ef] StrideArraysCore v0.4.7 [2e8cd123] StructuredArrays v0.2.22 [62fd8b95] TensorCore v0.1.1 [f8b46487] TestItemRunner v1.1.4 [1c621080] TestItems v1.0.0 [8290d209] ThreadingUtilities v0.5.5 ⌅ [06e1c1a7] TiledIteration v0.4.2 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [c3b1956e] TypeUtils v1.14.0 [3a884ed6] UnPack v1.0.2 [013be700] UnsafeAtomics v0.3.0 ⌃ [3d5dd08c] VectorizationBase v0.21.58 [efce3f68] WoodburyMatrices v1.1.0 [f5851436] FFTW_jll v3.3.11+0 [1d5cc7b8] IntelOpenMP_jll v2025.2.0+0 [856f044c] MKL_jll v2025.2.0+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [1317d2d5] oneTBB_jll v2022.0.0+1 [0dad84c5] ArgTools v1.1.1 [56f22d72] Artifacts [2a0f44e3] Base64 [ade2ca70] Dates [8ba89e20] Distributed [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching [9fa8497b] Future [b77e0a4c] InteractiveUtils [4af54fe1] LazyArtifacts [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 [8f399da3] Libdl [37e2e46d] LinearAlgebra [56ddb016] Logging [d6f4376e] Markdown [a63ad114] Mmap [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.10.0 [de0858da] Printf [3fa0cd96] REPL [9a3f8284] Random [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization [1a1011a3] SharedArrays [6462fe0b] Sockets [2f01184e] SparseArrays v1.10.0 [10745b16] Statistics v1.10.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test [cf7118a7] UUIDs [4ec0a83e] Unicode [e66e0078] CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] LibCURL_jll v8.4.0+0 [e37daf67] LibGit2_jll v1.6.4+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.1010+0 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.23+5 [05823500] OpenLibm_jll v0.8.5+0 [bea87d4a] SuiteSparse_jll v7.2.1+1 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.52.0+1 [3f19e933] p7zip_jll v17.4.0+2 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... ┌ Warning: Assignment to `B0` in soft scope is ambiguous because a global variable by the same name exists: `B0` will be treated as a new local. Disambiguate by using `local B0` to suppress this warning or `global B0` to assign to the existing global variable. └ @ ~/.julia/packages/MriResearchTools/xQXjo/test/methods.jl:47 Using 1 CPU threads Running 5 TGV iterations... 40%|█████████▋ | ETA: 0:00:08 Running 5 TGV iterations... 100%|████████████████████████| Time: 0:00:06 Using 1 CPU threads Using 1 CPU threads Using 1 CPU threads Using 1 CPU threads Using 1 CPU threads Using 1 CPU threads WARNING: Method definition boundscheck() in module StrideArraysCore at /home/pkgeval/.julia/packages/StrideArraysCore/lUhTe/src/ptr_array.jl:886 overwritten at /home/pkgeval/.julia/packages/StrideArraysCore/lUhTe/src/StrideArraysCore.jl:72. WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(MriResearchTools.qsm_average), AbstractArray{T, N} where N where T, AbstractArray{T, N} where N where T, AbstractArray{T, N} where N where T, Any, Any) in module QuantitativeSusceptibilityMappingTGVExt at /home/pkgeval/.julia/packages/MriResearchTools/xQXjo/ext/QSM_common.jl:1 overwritten in module QSMExt on the same line (check for duplicate calls to `include`). WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(MriResearchTools.qsm_mask_filled), AbstractArray{T, N} where N where T) in module QuantitativeSusceptibilityMappingTGVExt at /home/pkgeval/.julia/packages/MriResearchTools/xQXjo/ext/QSM_common.jl:37 overwritten in module QSMExt on the same line (check for duplicate calls to `include`). WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(MriResearchTools.qsm_mask_filled), AbstractArray{T, N} where N where T, Any) in module QuantitativeSusceptibilityMappingTGVExt at /home/pkgeval/.julia/packages/MriResearchTools/xQXjo/ext/QSM_common.jl:32 overwritten in module QSMExt on the same line (check for duplicate calls to `include`). WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(MriResearchTools.qsm_romeo_B0), AbstractArray{T, N} where N where T, Any, Any, Any, Any) in module QuantitativeSusceptibilityMappingTGVExt at /home/pkgeval/.julia/packages/MriResearchTools/xQXjo/ext/QSM_common.jl:5 overwritten in module QSMExt on the same line (check for duplicate calls to `include`). WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(MriResearchTools.qsm_laplacian_combine), AbstractArray{T, N} where N where T, Any, Any, Any, Any) in module QuantitativeSusceptibilityMappingTGVExt at /home/pkgeval/.julia/packages/MriResearchTools/xQXjo/ext/QSM_common.jl:18 overwritten in module QSMExt on the same line (check for duplicate calls to `include`). WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(MriResearchTools.qsm_B0), AbstractArray{T, N} where N where T, AbstractArray{T, N} where N where T, Any) in module QuantitativeSusceptibilityMappingTGVExt at /home/pkgeval/.julia/packages/MriResearchTools/xQXjo/ext/QuantitativeSusceptibilityMappingTGVExt.jl:13 overwritten in module QSMExt at /home/pkgeval/.julia/packages/MriResearchTools/xQXjo/ext/QSMExt.jl:29. WARNING: Method definition qsm_average(AbstractArray{T, N} where N where T, AbstractArray{T, N} where N where T, AbstractArray{T, N} where N where T, Any, Any) in module QuantitativeSusceptibilityMappingTGVExt at /home/pkgeval/.julia/packages/MriResearchTools/xQXjo/ext/QSM_common.jl:1 overwritten in module QSMExt on the same line (check for duplicate calls to `include`). WARNING: Method definition qsm_B0(AbstractArray{T, N} where N where T, AbstractArray{T, N} where N where T, Any) in module QuantitativeSusceptibilityMappingTGVExt at /home/pkgeval/.julia/packages/MriResearchTools/xQXjo/ext/QuantitativeSusceptibilityMappingTGVExt.jl:13 overwritten in module QSMExt at /home/pkgeval/.julia/packages/MriResearchTools/xQXjo/ext/QSMExt.jl:29. WARNING: Method definition qsm_laplacian_combine(AbstractArray{T, N} where N where T, Any, Any, Any, Any) in module QuantitativeSusceptibilityMappingTGVExt at /home/pkgeval/.julia/packages/MriResearchTools/xQXjo/ext/QSM_common.jl:18 overwritten in module QSMExt on the same line (check for duplicate calls to `include`). WARNING: Method definition qsm_romeo_B0(AbstractArray{T, N} where N where T, Any, Any, Any, Any) in module QuantitativeSusceptibilityMappingTGVExt at /home/pkgeval/.julia/packages/MriResearchTools/xQXjo/ext/QSM_common.jl:5 overwritten in module QSMExt on the same line (check for duplicate calls to `include`). WARNING: Method definition qsm_mask_filled(AbstractArray{T, N} where N where T) in module QuantitativeSusceptibilityMappingTGVExt at /home/pkgeval/.julia/packages/MriResearchTools/xQXjo/ext/QSM_common.jl:37 overwritten in module QSMExt on the same line (check for duplicate calls to `include`). WARNING: Method definition qsm_mask_filled(AbstractArray{T, N} where N where T, Any) in module QuantitativeSusceptibilityMappingTGVExt at /home/pkgeval/.julia/packages/MriResearchTools/xQXjo/ext/QSM_common.jl:32 overwritten in module QSMExt on the same line (check for duplicate calls to `include`). Test Summary: | Pass Total Time Package | 80 80 18m33.4s test/VSMbasedunwarping.jl | None 1m41.0s VSMbasedunwarping | None 1m40.9s test/intensitycorrection.jl | None 1m31.9s intensitycorrection | None 1m31.9s test/methods.jl | 24 24 1m46.0s methods | 24 24 1m46.0s test/qsm_tgv.jl | None 5m11.3s Test QuantitativeSusceptibilityMappingTGV integration | None 5m11.3s test/masking.jl | 9 9 1m58.1s Masking | 9 9 1m58.1s test/smoothing.jl | 7 7 21.4s Smoothing | 7 7 21.4s test/mcpc3ds.jl | None 2m28.2s mcpc3ds | None 2m28.2s test/unwrapping.jl | 7 7 40.5s unwrapping | 7 7 40.5s test/qsm.jl | None 2m24.5s Test QSM integration | None 2m24.5s test/utility.jl | 14 14 11.1s utility | 14 14 11.1s test/niftihandling.jl | 19 19 19.3s niftihandling | 19 19 19.3s Testing MriResearchTools tests passed Testing completed after 1152.07s PkgEval succeeded after 1743.18s