Package evaluation of HDF5 on Julia 1.13.0-DEV.897 (a39797a4fb*) started at 2025-07-24T14:12:25.492 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.47s ################################################################################ # Installation # Installing HDF5... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [f67ccb44] + HDF5 v0.17.2 Updating `~/.julia/environments/v1.13/Manifest.toml` [34da2185] + Compat v4.17.0 [f67ccb44] + HDF5 v0.17.2 [692b3bcd] + JLLWrappers v1.7.1 [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 v2.12.1+0 [7cb0a576] + MPICH_jll v4.3.1+0 [f1f71cc9] + MPItrampoline_jll v5.5.4+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [fe0851c0] + OpenMPI_jll v5.0.8+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 v1.7.0 [7b1f6079] + FileWatching v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [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 v1.3.0 [44cfe95a] + Pkg v1.13.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [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 v8.14.1+1 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.7.15 [458c3c95] + OpenSSL_jll v3.5.1+0 [efcefdf7] + PCRE2_jll v10.45.0+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 Installation completed after 8.44s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 24.86s ################################################################################ # Testing # Testing HDF5 Status `/tmp/jl_DQJkL1/Project.toml` [34da2185] Compat v4.17.0 [5789e2e9] FileIO v1.17.0 [f67ccb44] HDF5 v0.17.2 [da04e1cc] MPI v0.20.22 [3da0fdf6] MPIPreferences v0.1.11 [bac558e1] OrderedCollections v1.8.1 [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 v1.13.0 [a63ad114] Mmap v1.11.0 [44cfe95a] Pkg v1.13.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 Status `/tmp/jl_DQJkL1/Manifest.toml` [34da2185] Compat v4.17.0 [ffbed154] DocStringExtensions v0.9.5 [5789e2e9] FileIO v1.17.0 [f67ccb44] HDF5 v0.17.2 [692b3bcd] JLLWrappers v1.7.1 [da04e1cc] MPI v0.20.22 [3da0fdf6] MPIPreferences v0.1.11 [bac558e1] OrderedCollections v1.8.1 [eebad327] PkgVersion v0.3.3 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.4.3 [ae029012] Requires v1.3.1 [0234f1f7] HDF5_jll v1.14.6+0 [e33a78d0] Hwloc_jll v2.12.1+0 [7cb0a576] MPICH_jll v4.3.1+0 [f1f71cc9] MPItrampoline_jll v5.5.4+0 [9237b28f] MicrosoftMPI_jll v10.1.4+3 [fe0851c0] OpenMPI_jll v5.0.8+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 v1.7.0 [7b1f6079] FileWatching v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [4af54fe1] LazyArtifacts v1.11.0 [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 v8.14.1+1 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.7.15 [4536629a] OpenBLAS_jll v0.3.29+0 [458c3c95] OpenSSL_jll v3.5.1+0 [efcefdf7] PCRE2_jll v10.45.0+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 Testing Running tests... Resolving package versions... Updating `/tmp/jl_DQJkL1/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_DQJkL1/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_DQJkL1/Project.toml` [51b4e782] + H5Zbitshuffle v0.1.2 `~/.julia/packages/HDF5/Z859u/filters/H5Zbitshuffle` Updating `/tmp/jl_DQJkL1/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 packages... 9563.2 ms ✓ H5Zblosc 1 dependency successfully precompiled in 10 seconds. 46 already precompiled. Precompiling packages... 3272.9 ms ✓ CodecLz4 6263.5 ms ✓ H5Zlz4 2 dependencies successfully precompiled in 10 seconds. 47 already precompiled. Precompiling packages... 1845.2 ms ✓ CodecBzip2 6170.4 ms ✓ H5Zbzip2 2 dependencies successfully precompiled in 8 seconds. 47 already precompiled. Precompiling packages... 2647.7 ms ✓ CodecZstd 7026.1 ms ✓ H5Zzstd 2 dependencies successfully precompiled in 10 seconds. 48 already precompiled. Precompiling packages... 1684.1 ms ✓ bitshuffle_jll 5864.7 ms ✓ H5Zbitshuffle 2 dependencies successfully precompiled in 8 seconds. 44 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 └ @ Core ~/.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"#366#367")(h5f::HDF5.File) @ Main ~/.julia/packages/HDF5/Z859u/test/objects.jl:19 [2] (::HDF5.var"#21#22"{HDF5.HDF5Context, @Kwargs{}, var"#366#367", HDF5.File})() @ HDF5 ~/.julia/packages/HDF5/Z859u/src/file.jl:101 [3] task_local_storage(body::HDF5.var"#21#22"{HDF5.HDF5Context, @Kwargs{}, var"#366#367", HDF5.File}, key::Symbol, val::HDF5.HDF5Context) @ Base ./task.jl:298 [4] h5open(::var"#366#367", ::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] top-level scope @ ~/.julia/packages/HDF5/Z859u/test/objects.jl:6 [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1858 [inlined] [8] macro expansion @ ~/.julia/packages/HDF5/Z859u/test/objects.jl:16 [inlined] Precompiling packages... 11206.3 ms ✓ MPI 1 dependency successfully precompiled in 11 seconds. 41 already precompiled. Precompiling packages... 6769.4 ms ✓ HDF5 → MPIExt 1 dependency successfully precompiled in 7 seconds. 48 already precompiled. Test Summary: | Pass Fail Broken Total Time HDF5.jl | 1563 1 3 1567 6m19.3s plain | 151 1 152 1m04.9s complex | 13 13 5.4s undefined and null | 4 4 0.1s abstract arrays | 2 2 2.2s empty and 0-size arrays | 39 39 2.6s generic read of native types | 17 17 1.4s show | 51 51 11.2s split1 | 13 13 0.4s haskey | 18 18 1.3s AbstractString | 51 51 8.6s opaque data | 7 7 3.1s FixedStrings and FixedArrays | 18 18 3.4s Object Exists | 8 8 0.3s HDF5 existance | 4 4 0.4s bounds | 2 2 0.5s create_dataset | 352 352 3.3s Strings | 8 8 2.5s h5a_iterate | 8 8 0.4s h5l_iterate | 8 8 0.4s h5dchunk_iter | 3 3 0.0s compound | 10 10 9.6s create_dataset (compound) | 4 4 1.6s write_compound | 27 27 6.7s custom | 6 6 2.5s reference | 6 6 0.9s Dataspaces | 95 95 1.3s Datatypes | 15 15 0.2s BlockRange | 35 35 0.5s hyperslab | 5 5 3.0s read 0-length arrays: issue #859 | 0 0.6s attrs interface | 92 92 7.7s variable length strings | 1 1 0.3s readremote | 23 23 6.0s extend | 29 29 5.2s gc | 101 101 9.7s external | 6 6 0.1s swmr | 4 4 18.3s mmap | 9 9 3.5s properties | 46 1 47 5.1s filter | 81 81 26.6s Raw Chunk I/O | 80 80 15.4s fileio | 6 6 5.3s track order | 18 18 5.5s h5f_get_dset_no_attrs_hint | 6 6 0.9s non-allocating methods | 11 1 12 3.1s Compression Filter Unit Tests | 6 6 0.2s Object API | 37 1 38 7.5s virtual dataset | 5 5 2.3s mpio | 12 12 7.4s ros3 | 2 2 2.5s RNG of the outermost testset: Xoshiro(0x37a5862eeb77c430, 0x07bdcc346cc65ccc, 0x6bb03ab9f03e626c, 0x951cd19dd0c0491e, 0x7d19cbbe9844c682) 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 421.27s ERROR: LoadError: Package HDF5 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:2661 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2510 [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] 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 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [7] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:155 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [10] include(mod::Module, _path::String) @ Base ./Base.jl:311 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:320 [12] _start() @ Base ./client.jl:553 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 505.12s: package has test failures