Package evaluation of ImgCIFHandler on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T19:33:05.369 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.65s ################################################################################ # Installation # Installing ImgCIFHandler... Resolving package versions... Installed HDF5 ─ v0.16.16 Updating `~/.julia/environments/v1.11/Project.toml` [c7e9ad6d] + ImgCIFHandler v0.13.1 Updating `~/.julia/environments/v1.11/Manifest.toml` [621f4979] + AbstractFFTs v1.5.0 [79e6a3ab] + Adapt v4.3.0 [dce04be8] + ArgCheck v2.5.0 [4fba245c] + ArrayInterface v7.18.0 [a74b3585] + Blosc v0.7.3 ⌅ [fa961155] + CEnum v0.4.2 [aafaddc9] + CatIndices v0.2.2 ⌅ [523fee87] + CodecBzip2 v0.7.2 [6309b1aa] + CodecInflate64 v0.1.3 [5ba52731] + CodecLz4 v0.4.6 [944b1d66] + CodecZlib v0.7.8 ⌅ [6b39b394] + CodecZstd v0.7.2 ⌅ [3da002f7] + ColorTypes v0.11.5 ⌅ [c3611d14] + ColorVectorSpace v0.9.10 ⌅ [5ae59095] + Colors v0.12.11 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.16.0 [ed09eef8] + ComputationalResources v0.3.2 [a8cc5b0e] + Crayons v4.1.1 ⌅ [6007d9b0] + CrystalInfoFramework v0.8.0 [dc8bdbbb] + CustomUnitRanges v1.0.2 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [ffbed154] + DocStringExtensions v0.9.4 [4f61f5a4] + FFTViews v0.3.2 [7a1cc6ca] + FFTW v1.8.1 ⌅ [8fc22ac5] + FilePaths v0.8.3 [48062228] + FilePathsBase v0.9.24 [53c48c17] + FixedPointNumbers v0.8.5 [a2bd30eb] + Graphics v1.1.3 ⌃ [51b4e782] + H5Zbitshuffle v0.1.1 ⌃ [c8ec2601] + H5Zblosc v0.1.1 ⌃ [094576f2] + H5Zbzip2 v0.1.0 ⌃ [eb20ec05] + H5Zlz4 v0.1.0 ⌃ [f6f2d980] + H5Zzstd v0.1.0 ⌅ [f67ccb44] + HDF5 v0.16.16 [2c695a8d] + HistogramThresholding v0.3.1 [615f187c] + IfElse v0.1.1 ⌃ [c817782e] + ImageBase v0.1.5 ⌅ [cbc4b850] + ImageBinarization v0.2.9 ⌅ [a09fc81d] + ImageCore v0.9.4 ⌃ [6a3955dd] + ImageFiltering v0.7.6 [c7e9ad6d] + ImgCIFHandler v0.13.1 [842dd82b] + InlineStrings v1.4.3 [0c81fc1b] + InputBuffers v1.0.1 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.0 [b964fa9f] + LaTeXStrings v1.4.0 [d42ef402] + Lerche v0.5.6 [2ab3a3ac] + LogExpFunctions v0.3.29 [3da0fdf6] + MPIPreferences v0.1.11 [1914dd2f] + MacroTools v0.5.15 [dbb5928d] + MappedArrays v0.4.2 [e1d29d7a] + Missings v1.2.0 [e94cdb99] + MosaicViews v0.3.4 [77ba4419] + NaNMath v1.1.3 [6fe1bfb0] + OffsetArrays v1.16.0 [bac558e1] + OrderedCollections v1.8.0 [5432bcbf] + PaddedViews v0.5.12 ⌅ [f27b6e38] + Polynomials v3.2.13 [2dfb63ee] + PooledArrays v1.4.3 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [94ee1d12] + Quaternions v0.7.6 [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 [91c51154] + SentinelArrays v1.4.8 [777ac1f9] + SimpleBufferStream v1.2.0 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.0 [cae243ae] + StackViews v0.1.1 [aedffcd0] + Static v1.2.0 [0d7ed370] + StaticArrayInterface v1.8.0 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 [62fd8b95] + TensorCore v0.1.1 [06e1c1a7] + TiledIteration v0.5.0 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [5c2747f8] + URIs v1.5.2 [49080126] + ZipArchives v2.4.1 [0b7ba130] + Blosc_jll v1.21.7+0 [6e34b625] + Bzip2_jll v1.0.9+0 [9b99e207] + CBFlib_small_jll v0.9.6+0 [f5851436] + FFTW_jll v3.3.11+0 [0234f1f7] + HDF5_jll v1.14.6+0 [e33a78d0] + Hwloc_jll v2.12.0+0 ⌅ [a51ab1cf] + ICU_jll v69.1.0+0 [1d5cc7b8] + IntelOpenMP_jll v2025.0.4+0 [5ced341a] + Lz4_jll v1.10.1+0 [856f044c] + MKL_jll v2025.0.1+1 [7cb0a576] + MPICH_jll v4.3.0+1 [f1f71cc9] + MPItrampoline_jll v5.5.3+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [fe0851c0] + OpenMPI_jll v5.0.7+2 [458c3c95] + OpenSSL_jll v3.0.16+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [76ed43ae] + SQLite_jll v3.48.0+0 [3161d3a3] + Zstd_jll v1.5.7+1 ⌅ [228fe19c] + bitshuffle_jll v0.4.2+0 [6fcef0ae] + cif_api_jll v0.4.2+0 [477f73a3] + libaec_jll v1.1.3+0 [1317d2d5] + oneTBB_jll v2022.0.0+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [2f01184e] + SparseArrays 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 v1.1.1+0 [deac9b47] + LibCURL_jll v8.6.0+0 [e37daf67] + LibGit2_jll v1.7.2+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.6+0 [14a3606d] + MozillaCACerts_jll v2023.12.12 [4536629a] + OpenBLAS_jll v0.3.27+1 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.7.0+0 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.59.0+0 [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` Building HDF5 → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/114e20044677badbc631ee6fdc80a67920561a29/build.log` Installation completed after 12.12s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 252.18s ################################################################################ # Testing # Testing ImgCIFHandler ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1920 Status `/tmp/jl_5euEbI/Project.toml` ⌅ [6007d9b0] CrystalInfoFramework v0.8.0 [a93c6f00] DataFrames v1.7.0 ⌅ [8fc22ac5] FilePaths v0.8.3 [c7e9ad6d] ImgCIFHandler v0.13.1 [5c2747f8] URIs v1.5.2 [8dfed614] Test v1.11.0 Status `/tmp/jl_5euEbI/Manifest.toml` [621f4979] AbstractFFTs v1.5.0 [79e6a3ab] Adapt v4.3.0 [dce04be8] ArgCheck v2.5.0 [4fba245c] ArrayInterface v7.18.0 [a74b3585] Blosc v0.7.3 ⌅ [fa961155] CEnum v0.4.2 [aafaddc9] CatIndices v0.2.2 ⌅ [523fee87] CodecBzip2 v0.7.2 [6309b1aa] CodecInflate64 v0.1.3 [5ba52731] CodecLz4 v0.4.6 [944b1d66] CodecZlib v0.7.8 ⌅ [6b39b394] CodecZstd v0.7.2 ⌅ [3da002f7] ColorTypes v0.11.5 ⌅ [c3611d14] ColorVectorSpace v0.9.10 ⌅ [5ae59095] Colors v0.12.11 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.16.0 [ed09eef8] ComputationalResources v0.3.2 [a8cc5b0e] Crayons v4.1.1 ⌅ [6007d9b0] CrystalInfoFramework v0.8.0 [dc8bdbbb] CustomUnitRanges v1.0.2 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [ffbed154] DocStringExtensions v0.9.4 [4f61f5a4] FFTViews v0.3.2 [7a1cc6ca] FFTW v1.8.1 ⌅ [8fc22ac5] FilePaths v0.8.3 [48062228] FilePathsBase v0.9.24 [53c48c17] FixedPointNumbers v0.8.5 [a2bd30eb] Graphics v1.1.3 ⌃ [51b4e782] H5Zbitshuffle v0.1.1 ⌃ [c8ec2601] H5Zblosc v0.1.1 ⌃ [094576f2] H5Zbzip2 v0.1.0 ⌃ [eb20ec05] H5Zlz4 v0.1.0 ⌃ [f6f2d980] H5Zzstd v0.1.0 ⌅ [f67ccb44] HDF5 v0.16.16 [2c695a8d] HistogramThresholding v0.3.1 [615f187c] IfElse v0.1.1 ⌃ [c817782e] ImageBase v0.1.5 ⌅ [cbc4b850] ImageBinarization v0.2.9 ⌅ [a09fc81d] ImageCore v0.9.4 ⌃ [6a3955dd] ImageFiltering v0.7.6 [c7e9ad6d] ImgCIFHandler v0.13.1 [842dd82b] InlineStrings v1.4.3 [0c81fc1b] InputBuffers v1.0.1 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [b964fa9f] LaTeXStrings v1.4.0 [d42ef402] Lerche v0.5.6 [2ab3a3ac] LogExpFunctions v0.3.29 [3da0fdf6] MPIPreferences v0.1.11 [1914dd2f] MacroTools v0.5.15 [dbb5928d] MappedArrays v0.4.2 [e1d29d7a] Missings v1.2.0 [e94cdb99] MosaicViews v0.3.4 [77ba4419] NaNMath v1.1.3 [6fe1bfb0] OffsetArrays v1.16.0 [bac558e1] OrderedCollections v1.8.0 [5432bcbf] PaddedViews v0.5.12 ⌅ [f27b6e38] Polynomials v3.2.13 [2dfb63ee] PooledArrays v1.4.3 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [94ee1d12] Quaternions v0.7.6 [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 [91c51154] SentinelArrays v1.4.8 [777ac1f9] SimpleBufferStream v1.2.0 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.0 [cae243ae] StackViews v0.1.1 [aedffcd0] Static v1.2.0 [0d7ed370] StaticArrayInterface v1.8.0 [90137ffa] StaticArrays v1.9.13 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 [62fd8b95] TensorCore v0.1.1 [06e1c1a7] TiledIteration v0.5.0 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [5c2747f8] URIs v1.5.2 [49080126] ZipArchives v2.4.1 [0b7ba130] Blosc_jll v1.21.7+0 [6e34b625] Bzip2_jll v1.0.9+0 [9b99e207] CBFlib_small_jll v0.9.6+0 [f5851436] FFTW_jll v3.3.11+0 [0234f1f7] HDF5_jll v1.14.6+0 [e33a78d0] Hwloc_jll v2.12.0+0 ⌅ [a51ab1cf] ICU_jll v69.1.0+0 [1d5cc7b8] IntelOpenMP_jll v2025.0.4+0 [5ced341a] Lz4_jll v1.10.1+0 [856f044c] MKL_jll v2025.0.1+1 [7cb0a576] MPICH_jll v4.3.0+1 [f1f71cc9] MPItrampoline_jll v5.5.3+0 [9237b28f] MicrosoftMPI_jll v10.1.4+3 [fe0851c0] OpenMPI_jll v5.0.7+2 [458c3c95] OpenSSL_jll v3.0.16+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [76ed43ae] SQLite_jll v3.48.0+0 [3161d3a3] Zstd_jll v1.5.7+1 ⌅ [228fe19c] bitshuffle_jll v0.4.2+0 [6fcef0ae] cif_api_jll v0.4.2+0 [477f73a3] libaec_jll v1.1.3+0 [1317d2d5] oneTBB_jll v2022.0.0+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.11.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [2f01184e] SparseArrays 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 v1.1.1+0 [deac9b47] LibCURL_jll v8.6.0+0 [e37daf67] LibGit2_jll v1.7.2+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.6+0 [14a3606d] MozillaCACerts_jll v2023.12.12 [4536629a] OpenBLAS_jll v0.3.27+1 [05823500] OpenLibm_jll v0.8.5+0 [bea87d4a] SuiteSparse_jll v7.7.0+0 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.59.0+0 [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... Test variants of imgload: Error During Test at /home/pkgeval/.julia/packages/ImgCIFHandler/AzKl0/test/runtests.jl:31 Got exception outside of a @test IOError: could not spawn `bunzip2 -k /home/pkgeval/.julia/packages/ImgCIFHandler/AzKl0/test/testfiles/b4_mini.tar.bz2`: no such file or directory (ENOENT) Stacktrace: [1] _spawn_primitive(file::String, cmd::Cmd, stdio::Memory{Union{RawFD, Base.SyncCloseFD, IO}}) @ Base ./process.jl:140 [2] _spawn @ ./process.jl:157 [inlined] [3] #883 @ ./process.jl:149 [inlined] [4] setup_stdios(f::Base.var"#883#884"{Cmd}, stdios::Vector{Union{RawFD, Base.FileRedirect, IO}}) @ Base ./process.jl:236 [5] _spawn @ ./process.jl:148 [inlined] [6] run(::Cmd; wait::Bool) @ Base ./process.jl:512 [7] run @ ./process.jl:510 [inlined] [8] extract_files() @ Main ~/.julia/packages/ImgCIFHandler/AzKl0/test/runtests.jl:18 [9] macro expansion @ ~/.julia/packages/ImgCIFHandler/AzKl0/test/runtests.jl:32 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [11] top-level scope @ ~/.julia/packages/ImgCIFHandler/AzKl0/test/runtests.jl:32 [12] include(fname::String) @ Main ./sysimg.jl:38 [13] top-level scope @ none:6 [14] eval @ ./boot.jl:430 [inlined] [15] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [16] _start() @ Base ./client.jl:531 Test Summary: | Error Total Time Test variants of imgload | 1 1 3.8s ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/ImgCIFHandler/AzKl0/test/runtests.jl:31 Testing failed after 45.46s ERROR: LoadError: Package ImgCIFHandler errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.11/Pkg/src/Operations.jl:2124 [3] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2007 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.11/Pkg/src/API.jl:481 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 333.55s: package tests unexpectedly errored