Package evaluation of OMETIFF on Julia 1.13.0-DEV.1080 (ed57414aec*) started at 2025-09-04T17:11:50.566 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.78s ################################################################################ # Installation # Installing OMETIFF... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [2d0ec36b] + OMETIFF v0.4.5 Updating `~/.julia/environments/v1.13/Manifest.toml` [39de3d68] + AxisArrays v0.4.7 ⌅ [3da002f7] + ColorTypes v0.11.5 ⌃ [c3611d14] + ColorVectorSpace v0.10.0 [5ae59095] + Colors v0.13.1 [34da2185] + Compat v4.18.0 ⌅ [864edb3b] + DataStructures v0.18.22 [ffbed154] + DocStringExtensions v0.9.5 [8f5d6c58] + EzXML v1.2.2 [5789e2e9] + FileIO v1.17.0 [53c48c17] + FixedPointNumbers v0.8.5 [2803e5a7] + ImageAxes v0.6.12 [c817782e] + ImageBase v0.1.7 [a09fc81d] + ImageCore v0.10.5 [bc367c6b] + ImageMetadata v0.9.10 [9b13fd28] + IndirectArrays v1.0.0 [d25df0c9] + Inflate v0.1.5 [8197267c] + IntervalSets v0.7.11 [c8e1da08] + IterTools v1.10.0 [692b3bcd] + JLLWrappers v1.7.1 [682c06a0] + JSON v0.21.4 [1914dd2f] + MacroTools v0.5.16 [dbb5928d] + MappedArrays v0.4.2 [e94cdb99] + MosaicViews v0.3.4 [2d0ec36b] + OMETIFF v0.4.5 [6fe1bfb0] + OffsetArrays v1.17.0 [bac558e1] + OrderedCollections v1.8.1 [5432bcbf] + PaddedViews v0.5.12 [69de0a69] + Parsers v2.8.3 [eebad327] + PkgVersion v0.3.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [92933f4c] + ProgressMeter v1.11.0 [b3c3ace0] + RangeArrays v0.3.2 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [fdea26ae] + SIMD v3.7.1 [699a6c99] + SimpleTraits v0.9.5 [cae243ae] + StackViews v0.1.2 [10745b16] + Statistics v1.11.1 [62fd8b95] + TensorCore v0.1.1 ⌅ [731e570b] + TiffImages v0.9.1 [1986cc42] + Unitful v1.24.0 [94ce4f54] + Libiconv_jll v1.18.0+0 [02c8fc9c] + XML2_jll v2.14.4+0 [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 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [b27032c2] + LibCURL v0.6.4 [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 v1.13.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [f489334b] + StyledStrings v1.11.0 [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 v8.15.0+1 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.8.12 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.2+0 [efcefdf7] + PCRE2_jll v10.46.0+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.67.0+0 [3f19e933] + p7zip_jll v17.6.0+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 4.96s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 258.59s ################################################################################ # Testing # Testing OMETIFF Status `/tmp/jl_vstfhn/Project.toml` [39de3d68] AxisArrays v0.4.7 ⌅ [864edb3b] DataStructures v0.18.22 [ffbed154] DocStringExtensions v0.9.5 [8f5d6c58] EzXML v1.2.2 [5789e2e9] FileIO v1.17.0 [6218d12a] ImageMagick v1.4.2 [bc367c6b] ImageMetadata v0.9.10 [682c06a0] JSON v0.21.4 [2d0ec36b] OMETIFF v0.4.5 [92933f4c] ProgressMeter v1.11.0 [dca85d43] QuartzImageIO v0.7.5 ⌅ [731e570b] TiffImages v0.9.1 [1986cc42] Unitful v1.24.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 Status `/tmp/jl_vstfhn/Manifest.toml` [39de3d68] AxisArrays v0.4.7 ⌅ [3da002f7] ColorTypes v0.11.5 ⌃ [c3611d14] ColorVectorSpace v0.10.0 [5ae59095] Colors v0.13.1 [34da2185] Compat v4.18.0 ⌅ [864edb3b] DataStructures v0.18.22 [ffbed154] DocStringExtensions v0.9.5 [8f5d6c58] EzXML v1.2.2 [5789e2e9] FileIO v1.17.0 [53c48c17] FixedPointNumbers v0.8.5 [2803e5a7] ImageAxes v0.6.12 [c817782e] ImageBase v0.1.7 [a09fc81d] ImageCore v0.10.5 [6218d12a] ImageMagick v1.4.2 [bc367c6b] ImageMetadata v0.9.10 [9b13fd28] IndirectArrays v1.0.0 [d25df0c9] Inflate v0.1.5 [8197267c] IntervalSets v0.7.11 [c8e1da08] IterTools v1.10.0 [692b3bcd] JLLWrappers v1.7.1 [682c06a0] JSON v0.21.4 [1914dd2f] MacroTools v0.5.16 [dbb5928d] MappedArrays v0.4.2 [e94cdb99] MosaicViews v0.3.4 [2d0ec36b] OMETIFF v0.4.5 [6fe1bfb0] OffsetArrays v1.17.0 [bac558e1] OrderedCollections v1.8.1 [5432bcbf] PaddedViews v0.5.12 [69de0a69] Parsers v2.8.3 [eebad327] PkgVersion v0.3.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [92933f4c] ProgressMeter v1.11.0 [dca85d43] QuartzImageIO v0.7.5 [b3c3ace0] RangeArrays v0.3.2 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [fdea26ae] SIMD v3.7.1 [699a6c99] SimpleTraits v0.9.5 [cae243ae] StackViews v0.1.2 [10745b16] Statistics v1.11.1 [62fd8b95] TensorCore v0.1.1 ⌅ [731e570b] TiffImages v0.9.1 [1986cc42] Unitful v1.24.0 [6e34b625] Bzip2_jll v1.0.9+0 [f5851436] FFTW_jll v3.3.11+0 [61579ee1] Ghostscript_jll v9.55.1+0 [59f7168a] Giflib_jll v5.2.3+0 [c73af94c] ImageMagick_jll v7.1.2002+0 [aacddb02] JpegTurbo_jll v3.1.2+0 [88015f11] LERC_jll v4.0.1+0 [7e76a0d4] Libglvnd_jll v1.7.1+1 [94ce4f54] Libiconv_jll v1.18.0+0 [89763e89] Libtiff_jll v4.7.1+0 [d3a379c0] LittleCMS_jll v2.17.0+0 [643b3616] OpenJpeg_jll v2.5.4+0 [02c8fc9c] XML2_jll v2.14.4+0 [ffd25f8a] XZ_jll v5.8.1+0 [4f6342f7] Xorg_libX11_jll v1.8.12+0 [0c0b7dd1] Xorg_libXau_jll v1.0.13+0 [a3789734] Xorg_libXdmcp_jll v1.1.6+0 [1082639a] Xorg_libXext_jll v1.3.7+0 [c7cfdc94] Xorg_libxcb_jll v1.17.1+0 [c5fb5394] Xorg_xtrans_jll v1.6.0+0 [b53b4c65] libpng_jll v1.6.50+0 [c5f90fcd] libwebp_jll v1.6.0+0 [337d8026] libzip_jll v1.11.3+0 [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 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [b27032c2] LibCURL v0.6.4 [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 v1.13.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [f489334b] StyledStrings v1.11.0 [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 v8.15.0+1 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.8.12 [4536629a] OpenBLAS_jll v0.3.29+0 [458c3c95] OpenSSL_jll v3.5.2+0 [efcefdf7] PCRE2_jll v10.46.0+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.67.0+0 [3f19e933] p7zip_jll v17.6.0+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... Precompiling packages... 93206.0 ms ✓ TiffImages 5753.5 ms ✓ ImageAxes 4268.1 ms ✓ ImageMetadata Info Given OMETIFF was explicitly requested, output will be shown live  WARNING: Constructor for type "TiffFile" was extended in `OMETIFF` without explicit qualification or import.  NOTE: Assumed "TiffFile" refers to `TiffImages.TiffFile`. 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 TiffFile end`.  Hint: To silence the warning, qualify `TiffFile` as `TiffImages.TiffFile` in the method signature or explicitly `import TiffImages: TiffFile`. 22267.7 ms ✓ OMETIFF 4 dependencies successfully precompiled in 127 seconds. 75 already precompiled. 1 dependency had output during precompilation: ┌ OMETIFF │ [Output was shown above] └ Test Summary: | Pass Total Time TiffData Layouts | 13 13 19.1s Test Summary: | Pass Total Time Elapsed Time | 5 5 12.8s Cloning into 'exampletiffs'... Updating files: 75% (78/103) Updating files: 76% (79/103) Updating files: 77% (80/103) Updating files: 78% (81/103) Updating files: 79% (82/103) Updating files: 80% (83/103) Updating files: 81% (84/103) Updating files: 82% (85/103) Updating files: 83% (86/103) Updating files: 84% (87/103) Updating files: 85% (88/103) Updating files: 86% (89/103) Updating files: 87% (90/103) Updating files: 88% (91/103) Updating files: 89% (92/103) Updating files: 90% (93/103) Updating files: 91% (94/103) Updating files: 92% (95/103) Updating files: 93% (96/103) Updating files: 94% (97/103) Updating files: 95% (98/103) Updating files: 96% (99/103) Updating files: 97% (100/103) Updating files: 98% (101/103) Updating files: 99% (102/103) Updating files: 100% (103/103) Updating files: 100% (103/103), done. Progress: 10%|████▏ | ETA: 0:00:25 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Test Summary: | Pass Total Time Axes Values | 2 2 23.6s Progress: 78%|███████████████████████████████▉ | ETA: 0:00:00 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 Errors encountered while load Stream{DataFormat{:TIFF}, IOStream, String}(IOStream(), "/home/pkgeval/.julia/packages/OMETIFF/Jsw4Z/exampletiffs/ometiff_testdata/singles/181003_slices/P1_T0.tif"). All errors: =========================================== ArgumentError: Package ImageIO [82e4d734-157c-48bb-816b-45c225c6df19] is required but does not seem to be installed: - Run `Pkg.instantiate()` to install all recorded dependencies. =========================================== The value of field_readcount and field_writecount must be greater than or equal to -3 and not zero.. `TIFFMergeFieldInfo' @ error/tiff.c/TIFFErrors/575 =========================================== ArgumentError: Package OpenCV [f878e3a2-a245-4720-8660-60795d644f2a] is required but does not seem to be installed: - Run `Pkg.instantiate()` to install all recorded dependencies. =========================================== Fatal error: Intercalated IFDs, issue #19: Error During Test at /home/pkgeval/.julia/packages/OMETIFF/Jsw4Z/test/runtests.jl:97 Got exception outside of a @test MethodError: no method matching stacktrace(::Vector{Base.StackTraces.StackFrame}) The function `stacktrace` exists, but no method is defined for this combination of argument types. Closest candidates are: stacktrace(!Matched::Bool) @ Base stacktraces.jl:206 stacktrace() @ Base stacktraces.jl:206 stacktrace(!Matched::Vector{<:Union{Ptr{Nothing}, Base.InterpreterIP}}, !Matched::Bool) @ Base stacktraces.jl:193 ... Stacktrace: [1] CapturedException(ex::ArgumentError, bt_raw::Vector{Base.StackTraces.StackFrame}) @ Base ./task.jl:17 [2] handle_error(e::ArgumentError, q::Base.PkgId, bt::Vector{Union{Ptr{Nothing}, Base.InterpreterIP}}) @ FileIO ~/.julia/packages/FileIO/ePyCW/src/error_handling.jl:71 [3] handle_exceptions(exceptions::Vector{Tuple{Any, Union{Base.PkgId, Module}, Vector}}, action::String) @ FileIO ~/.julia/packages/FileIO/ePyCW/src/error_handling.jl:66 [4] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::Formatted; options::@Kwargs{}) @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:228 [5] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::Formatted) @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:196 [6] load(::Formatted; options::@Kwargs{}) @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:120 [7] load @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:116 [inlined] [8] (::var"#26#27")(s::IOStream) @ Main ~/.julia/packages/OMETIFF/Jsw4Z/test/runtests.jl:106 [9] open(f::var"#26#27", args::String; kwargs::@Kwargs{}) @ Base ./io.jl:420 [10] open @ ./io.jl:417 [inlined] [11] (::var"#24#25")(f::IOStream) @ Main ~/.julia/packages/OMETIFF/Jsw4Z/test/runtests.jl:105 [12] open(f::var"#24#25", args::String; kwargs::@Kwargs{}) @ Base ./io.jl:420 [13] open(f::Function, args::String) @ Base ./io.jl:417 [14] top-level scope @ ~/.julia/packages/OMETIFF/Jsw4Z/test/runtests.jl:47 [15] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1952 [inlined] [16] macro expansion @ ~/.julia/packages/OMETIFF/Jsw4Z/test/runtests.jl:98 [inlined] [17] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1952 [inlined] [18] macro expansion @ ~/.julia/packages/OMETIFF/Jsw4Z/test/runtests.jl:98 [inlined] [19] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:309 [20] top-level scope @ none:6 [21] eval(m::Module, e::Any) @ Core ./boot.jl:489 [22] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [23] _start() @ Base ./client.jl:563 Test Summary: | Pass Error Total Time Single file OME-TIFFs | 11 1 12 26.8s Single Channel OME-TIFF | 1 1 8.3s Multi Channel OME-TIFF | 2 2 1.1s Multi Channel Time Series OME-TIFF | 3 3 1.7s Multi Channel Z Series OME-TIFF | 3 3 0.9s Multi position OME-TIFF | 2 2 1.6s Intercalated IFDs, issue #19 | 1 1 13.2s RNG of the outermost testset: Random.Xoshiro(0x0e370ce5a19b5c9e, 0xa432d9ddc2b18f30, 0xa28fed1991e5d239, 0x9b61a7e1e4722b38, 0x674ad32c024c53d3) ERROR: LoadError: Some tests did not pass: 11 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/OMETIFF/Jsw4Z/test/runtests.jl:46 Testing failed after 251.36s ERROR: LoadError: Package OMETIFF errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/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/v1.13/Pkg/src/Operations.jl:2673 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2522 [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/v1.13/Pkg/src/API.jl:538 [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/v1.13/Pkg/src/API.jl:515 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:168 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:157 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [9] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:155 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:308 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:330 [14] _start() @ Base ./client.jl:563 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 551.92s: package tests unexpectedly errored