Package evaluation to test MRIFiles on Julia 1.14.0-DEV.1589 (2d9a3f8a61*) started at 2026-01-21T09:59:27.933 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 10.51s ################################################################################ # Installation # Installing MRIFiles... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [5a6f062f] + MRIFiles v0.3.2 Updating `~/.julia/environments/v1.14/Manifest.toml` [621f4979] + AbstractFFTs v1.5.0 [7f219486] + AbstractNFFTs v0.9.1 [34da2185] + Compat v4.18.1 [7a1cc6ca] + FFTW v1.10.0 [5789e2e9] + FileIO v1.17.1 [f67ccb44] + HDF5 v0.17.2 [076d061b] + HashArrayMappedTries v0.2.0 [692b3bcd] + JLLWrappers v1.7.1 [9c8b4983] + LightXML v0.9.3 [3da0fdf6] + MPIPreferences v0.1.11 [f7771a9a] + MRIBase v0.4.6 [5a6f062f] + MRIFiles v0.3.2 [7424e34d] + NFFTTools v0.2.7 [21216c6a] + Preferences v1.5.1 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [7e506255] + ScopedValues v1.5.0 [f5851436] + FFTW_jll v3.3.11+0 ⌅ [0234f1f7] + HDF5_jll v1.14.6+0 ⌃ [e33a78d0] + Hwloc_jll v2.12.1+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 [02c8fc9c] + XML2_jll v2.15.1+0 [477f73a3] + libaec_jll v1.1.4+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 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching 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 [f489334b] + StyledStrings v1.13.0 [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 v8.18.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [efcefdf7] + PCRE2_jll v10.47.0+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 9.08s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 2651.5 ms ✓ IntegralArrays 7632.7 ms ✓ PNGFiles 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. 5303.2 ms ✓ Interpolations 4888.5 ms ✓ Clustering 3288.8 ms ✓ HistogramThresholding 1539.2 ms ✓ ColorVectorSpace → SpecialFunctionsExt 8782.3 ms ✓ JpegTurbo 11998.8 ms ✓ Sixel 6297.7 ms ✓ OpenEXR 7730.8 ms ✓ ImageShow 9120.7 ms ✓ MetaGraphs 3862.5 ms ✓ SimpleWeightedGraphs 7517.4 ms ✓ RegularizedLeastSquares 3043.5 ms ✓ LinearOperatorCollection → LinearOperatorFFTWExt 16950.1 ms ✓ ImageMorphology 8932.6 ms ✓ WebP 88747.1 ms ✓ ImageFiltering 2325.9 ms ✓ MRIBase 12614.1 ms ✓ ImageMagick 4175.5 ms ✓ LinearOperatorCollection → LinearOperatorWaveletExt 7027.5 ms ✓ ImageTransformations 8122.9 ms ✓ ImageBinarization 3148.9 ms ✓ LinearOperatorCollection → LinearOperatorNFFTExt 5998.4 ms ✓ ImageDistances 27069.4 ms ✓ ImageCorners 17371.7 ms ✓ ImageSegmentation 4710.6 ms ✓ MRICoilSensitivities 6953.4 ms ✓ MRIFiles 7815.6 ms ✓ MRIOperators 7405.5 ms ✓ ImageContrastAdjustment 11075.2 ms ✓ MRIReco 25067.6 ms ✓ ImageQualityIndexes 26962.2 ms ✓ Images 31970.7 ms ✓ ImageUtils 34 dependencies successfully precompiled in 412 seconds. 277 already precompiled. 1 dependency had output during precompilation: ┌ Interpolations │ 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. └ Precompilation completed after 423.41s ################################################################################ # Testing # Testing MRIFiles Status `/tmp/jl_y6fRq3/Project.toml` [5789e2e9] FileIO v1.17.1 [f67ccb44] HDF5 v0.17.2 [8ad4436d] ImageUtils v0.2.12 [9c8b4983] LightXML v0.9.3 [f7771a9a] MRIBase v0.4.6 [c57eb701] MRICoilSensitivities v0.1.4 [5a6f062f] MRIFiles v0.3.2 [bdf86e05] MRIReco v0.9.2 [189a3867] Reexport v1.2.2 [6c6a2e73] Scratch v1.3.0 [4af54fe1] LazyArtifacts v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [de0858da] Printf v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_y6fRq3/Manifest.toml` [621f4979] AbstractFFTs v1.5.0 [7f219486] AbstractNFFTs v0.9.1 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.43 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [ec485272] ArnoldiMethod 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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... [ Info: The test data is located at /home/pkgeval/.julia/artifacts/4a7a5048b08057bc2e03c69b78296a2eb04edfdd. [ Info: If you want to check the output of the tests, please head to /home/pkgeval/.julia/scratchspaces/00000000-0000-0000-0000-000000000000/tmp. ┌ Info: Read parameters timing │ t1 = 4.632627659 └ t2 = 1.0e-5 ┌ Warning: 1st half of image are the REAL part and 2nd half is the imaginary └ @ MRIFiles ~/.julia/packages/MRIFiles/9hXgx/src/Bruker/Bruker.jl:424 [ Info: Bruker protocol name : T2_RARE Direct Reconstruction... 13%|███▋ | ETA: 0:01:01 Direct Reconstruction... 100%|███████████████████████████| Time: 0:00:09 [ Info: Bruker protocol name : FLASH [ Info: Bruker protocol name : FLASH Direct Reconstruction... 50%|█████████████▌ | ETA: 0:00:06 Direct Reconstruction... 100%|███████████████████████████| Time: 0:00:05 [ Info: Bruker protocol name : FLASH [ Info: read offset not performed (only phase + slice) [ Info: Reconstruction of 3DUTE [ Info: Bruker protocol name : UTE3D BrukerFile Reco: Error During Test at /home/pkgeval/.julia/packages/MRIFiles/9hXgx/test/testBrukerFile.jl:46 Got exception outside of a @test MethodError: no method matching zero(::Type{Any}) This error has been manually thrown, explicitly, so the method may exist but be intentionally marked as unimplemented. Closest candidates are: zero(::Type{Any}) @ Base missing.jl:106 zero(::Type{T}) where T>:Missing @ Base missing.jl:108 zero(!Matched::Type{Union{}}, Any...) @ Base number.jl:359 ... Stacktrace: [1] zero(::Type{Any}) @ Base ./missing.jl:106 [2] _qreltype(::Type{Any}) @ LinearAlgebra /opt/julia/share/julia/stdlib/v1.14/LinearAlgebra/src/qr.jl:341 [3] qr(A::Matrix{Any}, arg::ColumnNorm; kwargs::@Kwargs{}) @ LinearAlgebra /opt/julia/share/julia/stdlib/v1.14/LinearAlgebra/src/qr.jl:424 [4] qr(A::Matrix{Any}, arg::ColumnNorm) @ LinearAlgebra /opt/julia/share/julia/stdlib/v1.14/LinearAlgebra/src/qr.jl:422 [5] \(A::Adjoint{Float64, Matrix{Float64}}, B::Vector{AbstractFloat}) @ LinearAlgebra /opt/julia/share/julia/stdlib/v1.14/LinearAlgebra/src/generic.jl:1243 [6] precomputePolyInterp(win::Function, m::Int64, σ::Float32, T::Type) @ NFFT ~/.julia/packages/NFFT/4tey8/src/precomputation.jl:317 [7] precomputation(k::Matrix{Float32}, N::Tuple{Int64, Int64, Int64}, Ñ::Tuple{Int64, Int64, Int64}, params::NFFT.NFFTParams{Float32, 3}) @ NFFT ~/.julia/packages/NFFT/4tey8/src/precomputation.jl:385 [8] NFFT.NFFTPlan(k::Matrix{Float32}, N::Tuple{Int64, Int64, Int64}; dims::UnitRange{Int64}, fftflags::UInt32, kwargs::@Kwargs{m::Int64, σ::Float64, blocking::Bool}) @ NFFT ~/.julia/packages/NFFT/4tey8/src/implementation.jl:97 [9] NFFTPlan @ ~/.julia/packages/NFFT/4tey8/src/implementation.jl:73 [inlined] [10] macro expansion @ ~/.julia/packages/NFFT/4tey8/src/NFFT.jl:52 [inlined] [11] macro expansion @ ./timing.jl:503 [inlined] [12] #plan_nfft#70 @ ~/.julia/packages/NFFT/4tey8/src/NFFT.jl:51 [inlined] [13] kwcall(::@NamedTuple{m::Int64, σ::Float64, fftflags::UInt32, blocking::Bool}, ::typeof(AbstractNFFTs.plan_nfft), ::NFFT.NFFTBackend, ::Type{Array}, ::Matrix{Float32}, ::Tuple{Int64, Int64, Int64}) @ NFFT ~/.julia/packages/NFFT/4tey8/src/NFFT.jl:49 [14] plan_nfft(::Type, ::Matrix{Float32}, ::Vararg{Any}; kwargs::@Kwargs{m::Int64, σ::Float64, fftflags::UInt32, blocking::Bool}) @ AbstractNFFTs ~/.julia/packages/AbstractNFFTs/xXIFn/src/derived.jl:32 [15] plan_nfft @ ~/.julia/packages/AbstractNFFTs/xXIFn/src/derived.jl:32 [inlined] [16] LinearOperatorNFFTExt.NFFTOpImpl(shape::Tuple{Int64, Int64, Int64}, tr::Matrix{Float32}; toeplitz::Bool, oversamplingFactor::Float64, kernelSize::Int64, S::Type{Vector{ComplexF32}}, kargs::@Kwargs{fftflags::UInt32}) @ LinearOperatorNFFTExt ~/.julia/packages/LinearOperatorCollection/KDZHj/ext/LinearOperatorNFFTExt/NFFTOp.jl:47 [17] kwcall(::@NamedTuple{toeplitz::Bool, oversamplingFactor::Float64, kernelSize::Int64, S::DataType, fftflags::UInt32}, ::Type{LinearOperatorNFFTExt.NFFTOpImpl}, shape::Tuple{Int64, Int64, Int64}, tr::Matrix{Float32}) @ LinearOperatorNFFTExt ~/.julia/packages/LinearOperatorCollection/KDZHj/ext/LinearOperatorNFFTExt/NFFTOp.jl:44 [18] #NFFTOp#1 @ ~/.julia/packages/LinearOperatorCollection/KDZHj/ext/LinearOperatorNFFTExt/NFFTOp.jl:19 [inlined] [19] kwcall(::@NamedTuple{nodes::Matrix{Float32}, shape::Tuple{Int64, Int64, Int64}, S::DataType, fftflags::UInt32}, ::Type{NFFTOp}, ::Type{ComplexF32}) @ LinearOperatorNFFTExt ~/.julia/packages/LinearOperatorCollection/KDZHj/ext/LinearOperatorNFFTExt/NFFTOp.jl:16 [20] fourierEncodingOp(shape::Tuple{Int64, Int64, Int64}, tr::Trajectory{Float32}, opName::String; subsampleIdx::Vector{Int64}, slice::Int64, correctionMap::Vector{ComplexF32}, echoImage::Bool, S::Type, copyOpsFn::Function, kargs::@Kwargs{}) @ MRIOperators ~/.julia/packages/MRIOperators/li8lA/src/EncodingOp.jl:167 [21] fourierEncodingOp @ ~/.julia/packages/MRIOperators/li8lA/src/EncodingOp.jl:140 [inlined] [22] #79 @ ./none:-1 [inlined] [23] iterate @ ./generator.jl:48 [inlined] [24] collect(itr::Base.Generator{UnitRange{Int64}, MRIOperators.var"#79#80"{@Kwargs{slice::Int64, correctionMap::Vector{ComplexF32}, S::DataType}, Tuple{Int64, Int64, Int64}, Vector{Vector{Int64}}, Vector{Trajectory{Float32}}}}) @ Base ./array.jl:828 [25] encodingOps_simple(acqData::AcquisitionData{Float32, 3}, shape::Tuple{Int64, Int64, Int64}; kargs::@Kwargs{slice::Int64, correctionMap::Vector{ComplexF32}, S::DataType}) @ MRIOperators ~/.julia/packages/MRIOperators/li8lA/src/EncodingOp.jl:19 [26] kwcall(::@NamedTuple{slice::Int64, correctionMap::Vector{ComplexF32}, S::DataType}, ::typeof(encodingOps_simple), acqData::AcquisitionData{Float32, 3}, shape::Tuple{Int64, Int64, Int64}) @ MRIOperators ~/.julia/packages/MRIOperators/li8lA/src/EncodingOp.jl:15 [27] reconstruction_direct(acqData::AcquisitionData{Float32, 3}, reconSize::Tuple{Int64, Int64, Int64}, weights::Vector{Vector{ComplexF32}}, correctionMap::Vector{ComplexF32}, arrayType::Type{Array}, S::Type) @ MRIReco ~/.julia/packages/MRIReco/XF7fg/src/Reconstruction/DirectReconstruction.jl:31 [28] reconstruction(acqData::AcquisitionData{Float32, 3}, recoParams::Dict{Symbol, Any}) @ MRIReco ~/.julia/packages/MRIReco/XF7fg/src/Reconstruction/Reconstruction.jl:40 [29] macro expansion @ ~/.julia/packages/MRIFiles/9hXgx/test/testBrukerFile.jl:129 [inlined] [30] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [31] macro expansion @ ~/.julia/packages/MRIFiles/9hXgx/test/testBrukerFile.jl:47 [inlined] [32] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [33] top-level scope @ ~/.julia/packages/MRIFiles/9hXgx/test/testBrukerFile.jl:3 [34] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [35] top-level scope @ ~/.julia/packages/MRIFiles/9hXgx/test/runtests.jl:13 [36] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [37] top-level scope @ none:6 [38] eval(m::Module, e::Any) @ Core ./boot.jl:489 [39] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [40] _start() @ Base ./client.jl:585 Test Summary: | Pass Error Total Time BrukerFile | 16 1 17 7m20.4s BrukerFile read parameters | 7 7 5.6s BrukerFile read 2dseq | 3 3 5.8s BrukerFile Reco | 6 1 7 7m08.9s RNG of the outermost testset: Random.Xoshiro(0x6bb07b44864a71e1, 0xe268f8a6525f1075, 0xd9f86bf99593e61a, 0x9f569ddd8cfaf49f, 0xb023d2264427d21b) ERROR: LoadError: Some tests did not pass: 16 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/MRIFiles/9hXgx/test/testBrukerFile.jl:1 in expression starting at /home/pkgeval/.julia/packages/MRIFiles/9hXgx/test/runtests.jl:13 Testing failed after 496.29s ERROR: LoadError: Package MRIFiles errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/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/v1.14/Pkg/src/Operations.jl:3122 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2987 [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/v1.14/Pkg/src/API.jl:572 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:548 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 977.5s: package tests unexpectedly errored