Package evaluation to test EMIRT on Julia 1.14.0-DEV.1372 (893635dc59*) started at 2025-12-16T16:14:38.669 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 9.65s ################################################################################ # Installation # Installing EMIRT... Resolving package versions... Installed HDF5 ─ v0.13.6 Updating `~/.julia/environments/v1.14/Project.toml` [8acf8dda] + EMIRT v0.7.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [a74b3585] + Blosc v0.7.3 ⌅ [3da002f7] + ColorTypes v0.7.5 ⌅ [5ae59095] + Colors v0.9.5 [8acf8dda] + EMIRT v0.7.0 [5789e2e9] + FileIO v1.17.1 ⌅ [53c48c17] + FixedPointNumbers v0.5.3 ⌅ [f67ccb44] + HDF5 v0.13.6 [692b3bcd] + JLLWrappers v1.7.1 [3da0fdf6] + MPIPreferences v0.1.11 [21216c6a] + Preferences v1.5.0 ⌅ [189a3867] + Reexport v0.2.0 [ae029012] + Requires v1.3.1 [0b7ba130] + Blosc_jll v1.21.7+0 ⌅ [0234f1f7] + HDF5_jll v1.14.6+0 [e33a78d0] + Hwloc_jll v2.12.2+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [5ced341a] + Lz4_jll v1.10.1+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 v2.13.9+0 [a65dc6b1] + Xorg_libpciaccess_jll v0.18.1+0 [477f73a3] + libaec_jll v1.1.4+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 v1.13.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [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 [6462fe0b] + Sockets v1.11.0 [f489334b] + StyledStrings v1.13.0 [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 v8.17.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.12.2 [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 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Building HDF5 → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/0713cbabdf855852dfab3ce6447c87145f3d9ea8/build.log` Installation completed after 15.84s ################################################################################ # Precompilation # ERROR: LoadError: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Nothing) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:10 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/precompile.jl:6 caused by: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Base.DevNull) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:7 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:577 Precompilation failed after 13.44s ################################################################################ # Testing # Testing EMIRT Status `/tmp/jl_eLR4Cf/Project.toml` ⌅ [5ae59095] Colors v0.9.5 [8acf8dda] EMIRT v0.7.0 [5789e2e9] FileIO v1.17.1 ⌅ [53c48c17] FixedPointNumbers v0.5.3 ⌅ [f67ccb44] HDF5 v0.13.6 [8ba89e20] Distributed v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_eLR4Cf/Manifest.toml` [a74b3585] Blosc v0.7.3 ⌅ [3da002f7] ColorTypes v0.7.5 ⌅ [5ae59095] Colors v0.9.5 [8acf8dda] EMIRT v0.7.0 [5789e2e9] FileIO v1.17.1 ⌅ [53c48c17] FixedPointNumbers v0.5.3 ⌅ [f67ccb44] HDF5 v0.13.6 [692b3bcd] JLLWrappers v1.7.1 [3da0fdf6] MPIPreferences v0.1.11 [21216c6a] Preferences v1.5.0 ⌅ [189a3867] Reexport v0.2.0 [ae029012] Requires v1.3.1 [0b7ba130] Blosc_jll v1.21.7+0 ⌅ [0234f1f7] HDF5_jll v1.14.6+0 [e33a78d0] Hwloc_jll v2.12.2+0 [94ce4f54] Libiconv_jll v1.18.0+0 [5ced341a] Lz4_jll v1.10.1+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 v2.13.9+0 [a65dc6b1] Xorg_libpciaccess_jll v0.18.1+0 [477f73a3] libaec_jll v1.1.4+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 v1.13.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v1.0.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [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 [6462fe0b] Sockets v1.11.0 [f489334b] StyledStrings v1.13.0 [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 v8.17.0+0 [e37daf67] LibGit2_jll v1.9.2+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [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 [8e850ede] nghttp2_jll v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... WARNING: Constructor for type "Array" was extended in `HDF5` without explicit qualification or import.  NOTE: Assumed "Array" refers to `Base.Array`. 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 Array end`.  Hint: To silence the warning, qualify `Array` as `Base.Array` in the method signature or explicitly `import Base: Array`. 1 dependency had output during precompilation: ┌ HDF5 │ WARNING: Constructor for type "Array" was extended in `HDF5` without explicit qualification or import. │ NOTE: Assumed "Array" refers to `Base.Array`. 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 Array end`. │ Hint: To silence the warning, qualify `Array` as `Base.Array` in the method signature or explicitly `import Base: Array`. └ ┌ Warning: The call to compilecache failed to create a usable precompiled cache file for EMIRT [8acf8dda-514d-5c36-9488-7e3496cf596e] │ exception = Required dependency Base.PkgId(Base.UUID("3da0fdf6-3ccc-4f1b-acd9-58baa6c99267"), "MPIPreferences") failed to load from a cache file. └ @ Base loading.jl:2891 WARNING: Constructor for type "Array" was extended in `HDF5` without explicit qualification or import.  NOTE: Assumed "Array" refers to `Base.Array`. 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 Array end`.  Hint: To silence the warning, qualify `Array` as `Base.Array` in the method signature or explicitly `import Base: Array`. 1 dependency had output during precompilation: ┌ HDF5 │ [Output was shown above] └ ┌ Warning: The call to compilecache failed to create a usable precompiled cache file for HDF5 [f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f] │ exception = Required dependency Base.PkgId(Base.UUID("3da0fdf6-3ccc-4f1b-acd9-58baa6c99267"), "MPIPreferences") failed to load from a cache file. └ @ Base loading.jl:2891 WARNING: Constructor for type "Array" was extended in `HDF5` without explicit qualification or import. NOTE: Assumed "Array" refers to `Base.Array`. 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 Array end`. Hint: To silence the warning, qualify `Array` as `Base.Array` in the method signature or explicitly `import Base: Array`. Test Summary: | Pass Total Time test IO | 6 6 12.1s reading file: /home/pkgeval/.julia/packages/EMIRT/C3RK2/test/../assets/aff.h5 ......done :) reading file: /home/pkgeval/.julia/packages/EMIRT/C3RK2/test/../assets/lbl.h5 ......done :) judec = Dict{Symbol, Float32}(:VIFSs => 0.652092, :ri => 0.9090549, :VIm => 0.013707907, :VIFS => 0.7800202, :rem => 0.00040644547, :VI => 0.2534154, :res => 0.09053864, :rfm => 0.99934626, :rf => 0.9318043, :VIS => -0.2534154, :VIFSm => 0.9703931, :re => 0.09094509, :rfs => 0.8728142, :ris => 0.2877324, :VIs => 0.2397075, :rim => 0.6213225) 0.004147 seconds (25.74 k allocations: 415.250 KiB) ecd = Dict{Symbol, Float32}(:VIFSs => 1.0000002, :ri => 1.0, :VIm => 0.0, :VIFS => 1.0000002, :rem => 0.0, :VI => -1.7881393f-7, :res => 0.0, :rfm => 1.0, :rf => 1.0, :VIS => 1.7881393f-7, :VIFSm => 1.0000002, :re => 0.0, :rfs => 1.0, :ris => 0.28813884, :VIs => 0.0, :rim => 0.71186113) 0.310376 seconds (1.06 M allocations: 22.346 MiB) ecd = Dict{Symbol, Float32}(:VIFSs => 0.045672167, :ri => 0.28817847, :VIm => 0.0, :VIFS => 0.08735393, :rem => 0.0, :VI => 9.672652, :res => 0.7118215, :rfm => 1.0, :rf => 0.00011138609, :VIS => -9.672652, :VIFSm => 0.9998097, :re => 0.7118215, :rfs => 5.569615f-5, :ris => 0.28813884, :VIs => 9.672761, :rim => 3.9647926f-5) Test Summary: | Pass Total Time test evaluate | 2 2 9.1s test segmentation downsampling create random segmentation for tests test creating fake mst ... test relabel_seg .... 1.128360 seconds (191.97 k allocations: 140.109 MiB, 1.98% gc time, 53.92% compilation time) test segid1N! ... test modified serial version ... 11.059015 seconds (65.11 k allocations: 561.477 MiB, 4.17% gc time, 1.46% compilation time) test modified serial version ... 11.250141 seconds (43 allocations: 558.025 MiB, 6.79% gc time) test mask singletons ... test removing singletons by masking ... 2.596431 seconds (17.09 M allocations: 327.900 MiB, 3.60% gc time, 8.09% compilation time) 1.910666 seconds (17.05 M allocations: 325.287 MiB, 19.11% gc time, 1.78% compilation time) Test Summary: | Pass Total Time test segmentations | 2 2 30.5s transform affinitymap to edge list... 0.193287 seconds (3 allocations: 8.766 MiB, 24.38% gc time) 1.364545 seconds (686.64 k allocations: 75.724 MiB, 3.45% gc time, 83.74% compilation time) segment affinity map using connectivity analysis ... 0.030286 seconds (35 allocations: 6.033 MiB) transform to uniform distribution ... map to uniform distribution...get the permutation by sorting...... 0.138403 seconds (6 allocations: 9.000 MiB) done :) done! 1.335862 seconds (730.67 k allocations: 68.115 MiB, 87.75% compilation time) exchange x and z axis of affinity map... exchange x and z of affinity map 0.391564 seconds (268.97 k allocations: 17.681 MiB, 98.90% compilation time) Test Summary: | Total Time test affinitymap | 0 3.2s Testing EMIRT tests passed Testing completed after 128.41s PkgEval succeeded after 177.55s