Package evaluation of HDF5 on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T10:15:38.384 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.95s ################################################################################ # Installation # Installing HDF5... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [f67ccb44] + HDF5 v0.17.2 Updating `~/.julia/environments/v1.11/Manifest.toml` [34da2185] + Compat v4.16.0 [f67ccb44] + HDF5 v0.17.2 [692b3bcd] + JLLWrappers v1.7.0 [3da0fdf6] + MPIPreferences v0.1.11 [21216c6a] + Preferences v1.4.3 [ae029012] + Requires v1.3.1 [0234f1f7] + HDF5_jll v1.14.6+0 [e33a78d0] + Hwloc_jll v2.12.0+0 [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 [477f73a3] + libaec_jll v1.1.3+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 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v0.6.4 [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 v1.2.0 [44cfe95a] + Pkg v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.1.1+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 [83775a58] + Zlib_jll v1.2.13+1 [8e850ede] + nghttp2_jll v1.59.0+0 [3f19e933] + p7zip_jll v17.4.0+2 Installation completed after 6.14s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 19.79s ################################################################################ # Testing # Testing HDF5 Status `/tmp/jl_1yNgkS/Project.toml` [34da2185] Compat v4.16.0 [5789e2e9] FileIO v1.17.0 [f67ccb44] HDF5 v0.17.2 [da04e1cc] MPI v0.20.22 [3da0fdf6] MPIPreferences v0.1.11 [bac558e1] OrderedCollections v1.8.0 [21216c6a] Preferences v1.4.3 [ae029012] Requires v1.3.1 [0234f1f7] HDF5_jll v1.14.6+0 [8bf52ea8] CRC32c v1.11.0 [8ba89e20] Distributed v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [a63ad114] Mmap v1.11.0 [44cfe95a] Pkg v1.11.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 Status `/tmp/jl_1yNgkS/Manifest.toml` [34da2185] Compat v4.16.0 [ffbed154] DocStringExtensions v0.9.4 [5789e2e9] FileIO v1.17.0 [f67ccb44] HDF5 v0.17.2 [692b3bcd] JLLWrappers v1.7.0 [da04e1cc] MPI v0.20.22 [3da0fdf6] MPIPreferences v0.1.11 [bac558e1] OrderedCollections v1.8.0 [eebad327] PkgVersion v0.3.3 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [ae029012] Requires v1.3.1 [0234f1f7] HDF5_jll v1.14.6+0 [e33a78d0] Hwloc_jll v2.12.0+0 [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 [477f73a3] libaec_jll v1.1.3+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [8bf52ea8] CRC32c v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching 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 [6462fe0b] Sockets 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 [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 ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Resolving package versions... Updating `/tmp/jl_1yNgkS/Project.toml` [c8ec2601] + H5Zblosc v0.1.2 `~/.julia/packages/HDF5/Z859u/filters/H5Zblosc` [094576f2] + H5Zbzip2 v0.1.1 `~/.julia/packages/HDF5/Z859u/filters/H5Zbzip2` [eb20ec05] + H5Zlz4 v0.1.1 `~/.julia/packages/HDF5/Z859u/filters/H5Zlz4` [f6f2d980] + H5Zzstd v0.1.1 `~/.julia/packages/HDF5/Z859u/filters/H5Zzstd` Updating `/tmp/jl_1yNgkS/Manifest.toml` [a74b3585] + Blosc v0.7.3 ⌅ [fa961155] + CEnum v0.4.2 ⌅ [523fee87] + CodecBzip2 v0.7.2 [5ba52731] + CodecLz4 v0.4.6 ⌅ [6b39b394] + CodecZstd v0.7.2 [c8ec2601] + H5Zblosc v0.1.2 `~/.julia/packages/HDF5/Z859u/filters/H5Zblosc` [094576f2] + H5Zbzip2 v0.1.1 `~/.julia/packages/HDF5/Z859u/filters/H5Zbzip2` [eb20ec05] + H5Zlz4 v0.1.1 `~/.julia/packages/HDF5/Z859u/filters/H5Zlz4` [f6f2d980] + H5Zzstd v0.1.1 `~/.julia/packages/HDF5/Z859u/filters/H5Zzstd` ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [0b7ba130] + Blosc_jll v1.21.7+0 [6e34b625] + Bzip2_jll v1.0.9+0 [5ced341a] + Lz4_jll v1.10.1+0 [3161d3a3] + Zstd_jll v1.5.7+1 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Resolving package versions... Updating `/tmp/jl_1yNgkS/Project.toml` [51b4e782] + H5Zbitshuffle v0.1.2 `~/.julia/packages/HDF5/Z859u/filters/H5Zbitshuffle` Updating `/tmp/jl_1yNgkS/Manifest.toml` [51b4e782] + H5Zbitshuffle v0.1.2 `~/.julia/packages/HDF5/Z859u/filters/H5Zbitshuffle` ⌅ [228fe19c] + bitshuffle_jll v0.4.2+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` [ Info: libhdf5 v1.14.6 Precompiling H5Zblosc... 4666.7 ms ✓ H5Zblosc 1 dependency successfully precompiled in 5 seconds. 45 already precompiled. Precompiling H5Zlz4... 3020.9 ms ✓ CodecLz4 4009.3 ms ✓ H5Zlz4 2 dependencies successfully precompiled in 8 seconds. 46 already precompiled. Precompiling H5Zbzip2... 914.2 ms ✓ CodecBzip2 3542.7 ms ✓ H5Zbzip2 2 dependencies successfully precompiled in 5 seconds. 46 already precompiled. Precompiling H5Zzstd... 1990.5 ms ✓ CodecZstd 3373.0 ms ✓ H5Zzstd 2 dependencies successfully precompiled in 6 seconds. 47 already precompiled. Precompiling H5Zbitshuffle... 1005.0 ms ✓ bitshuffle_jll 3310.1 ms ✓ H5Zbitshuffle 2 dependencies successfully precompiled in 4 seconds. 43 already precompiled. ┌ Warning: `filter=(307, 0)` keyword option is deprecated, use `filters=(307, 0)` instead │ caller = setproperty!(p::HDF5.DatasetCreateProperties, name::Symbol, val::Tuple{Int32, Int64}) at properties.jl:59 └ @ HDF5 ~/.julia/packages/HDF5/Z859u/src/properties.jl:59 ┌ Warning: `append!(filters::Filters.FilterPipeline, extra::NTuple{N, Integer}) where N` is deprecated, use `append!(filters, [ExternalFilter(extra...)])` instead. │ caller = set_filters! at properties.jl:499 [inlined] └ @ Core ~/.julia/packages/HDF5/Z859u/src/properties.jl:499 Object API: Test Failed at /home/pkgeval/.julia/packages/HDF5/Z859u/test/objects.jl:19 Expression: API.h5o_exists_by_name(h5f, "noonian") Expected: HDF5.API.H5Error No exception thrown Stacktrace: [1] (::var"#413#415")(h5f::HDF5.File) @ Main ~/.julia/packages/HDF5/Z859u/test/objects.jl:19 [2] (::HDF5.var"#17#18"{HDF5.HDF5Context, @Kwargs{}, var"#413#415", HDF5.File})() @ HDF5 ~/.julia/packages/HDF5/Z859u/src/file.jl:101 [3] task_local_storage(body::HDF5.var"#17#18"{HDF5.HDF5Context, @Kwargs{}, var"#413#415", HDF5.File}, key::Symbol, val::HDF5.HDF5Context) @ Base ./task.jl:315 [4] h5open(::var"#413#415", ::String, ::Vararg{String}; context::HDF5.HDF5Context, pv::@Kwargs{}) @ HDF5 ~/.julia/packages/HDF5/Z859u/src/file.jl:96 [5] h5open(::Function, ::String, ::String) @ HDF5 ~/.julia/packages/HDF5/Z859u/src/file.jl:94 [6] macro expansion @ ~/.julia/packages/HDF5/Z859u/test/objects.jl:16 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [8] top-level scope @ ~/.julia/packages/HDF5/Z859u/test/objects.jl:6 Precompiling MPIExt... 5034.1 ms ✓ HDF5 → MPIExt 1 dependency successfully precompiled in 5 seconds. 47 already precompiled. Test Summary: | Pass Fail Broken Total Time HDF5.jl | 1563 1 3 1567 5m42.5s plain | 151 1 152 1m07.6s complex | 13 13 4.5s undefined and null | 4 4 0.2s abstract arrays | 2 2 2.0s empty and 0-size arrays | 39 39 2.0s generic read of native types | 17 17 1.9s show | 51 51 9.8s split1 | 13 13 0.6s haskey | 18 18 1.3s AbstractString | 51 51 12.4s opaque data | 7 7 3.5s FixedStrings and FixedArrays | 18 18 3.8s Object Exists | 8 8 0.2s HDF5 existance | 4 4 0.1s bounds | 2 2 0.4s create_dataset | 352 352 3.8s Strings | 8 8 2.5s h5a_iterate | 8 8 0.5s h5l_iterate | 8 8 0.5s h5dchunk_iter | 3 3 0.0s compound | 10 10 9.5s create_dataset (compound) | 4 4 1.7s write_compound | 27 27 7.3s custom | 6 6 2.7s reference | 6 6 1.2s Dataspaces | 95 95 1.5s Datatypes | 15 15 0.2s BlockRange | 35 35 0.6s hyperslab | 5 5 2.7s read 0-length arrays: issue #859 | 0 0.8s attrs interface | 92 92 6.8s variable length strings | 1 1 0.2s readremote | 23 23 8.9s extend | 29 29 6.0s gc | 101 101 6.3s external | 6 6 0.2s swmr | 4 4 16.3s mmap | 9 9 2.9s properties | 46 1 47 4.1s filter | 81 81 24.3s Raw Chunk I/O | 80 80 13.0s fileio | 6 6 3.5s track order | 18 18 5.4s h5f_get_dset_no_attrs_hint | 6 6 0.7s non-allocating methods | 11 1 12 3.7s Compression Filter Unit Tests | 6 6 0.2s Object API | 37 1 38 5.0s virtual dataset | 5 5 1.8s mpio | 12 12 6.8s ros3 | 2 2 2.6s ERROR: LoadError: Some tests did not pass: 1563 passed, 1 failed, 0 errored, 3 broken. in expression starting at /home/pkgeval/.julia/packages/HDF5/Z859u/test/runtests.jl:34 Testing failed after 361.32s ERROR: LoadError: Package HDF5 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 432.89s: package has test failures