Package evaluation of AbstractGPs on Julia 1.12.0-rc1.2 (995ff9db19*) started at 2025-07-14T16:47:34.410 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.02s ################################################################################ # Installation # Installing AbstractGPs... Resolving package versions... Installed Rmath ─────────────────── v0.8.0 Installed StatsFuns ─────────────── v1.5.0 Installed HypergeometricFunctions ─ v0.3.28 Installed IrrationalConstants ───── v0.2.4 Installed PtrArrays ─────────────── v1.3.0 Installed TensorCore ────────────── v0.1.1 Installed Functors ──────────────── v0.5.2 Installed Preferences ───────────── v1.4.3 Installed DataAPI ───────────────── v1.16.0 Installed PDMats ────────────────── v0.11.35 Installed RecipesBase ───────────── v1.3.4 Installed ConstructionBase ──────── v1.6.0 Installed JLLWrappers ───────────── v1.7.0 Installed OrderedCollections ────── v1.8.1 Installed SpecialFunctions ──────── v2.5.1 Installed PrecompileTools ───────── v1.3.2 Installed Reexport ──────────────── v1.2.2 Installed QuadGK ────────────────── v2.11.2 Installed Statistics ────────────── v1.11.1 Installed FillArrays ────────────── v1.13.0 Installed Rmath_jll ─────────────── v0.5.1+0 Installed ChainRulesCore ────────── v1.25.2 Installed KernelFunctions ───────── v0.10.65 Installed Requires ──────────────── v1.3.1 Installed AliasTables ───────────── v1.1.3 Installed LogExpFunctions ───────── v0.3.29 Installed MacroTools ────────────── v0.5.16 Installed ZygoteRules ───────────── v0.2.7 Installed DataStructures ────────── v0.18.22 Installed AbstractGPs ───────────── v0.5.24 Installed StatsAPI ──────────────── v1.7.1 Installed Compat ────────────────── v4.17.0 Installed CompositionsBase ──────── v0.1.2 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed Distances ─────────────── v0.10.12 Installed Missings ──────────────── v1.2.0 Installed StatsBase ─────────────── v0.34.5 Installed SortingAlgorithms ─────── v1.2.1 Installed DocStringExtensions ───── v0.9.5 Installed Distributions ─────────── v0.25.120 Installing 2 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 KiB Updating `~/.julia/environments/v1.12/Project.toml` [99985d1d] + AbstractGPs v0.5.24 Updating `~/.julia/environments/v1.12/Manifest.toml` [99985d1d] + AbstractGPs v0.5.24 [66dad0bd] + AliasTables v1.1.3 [d360d2e6] + ChainRulesCore v1.25.2 [34da2185] + Compat v4.17.0 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.13.0 [d9f16b24] + Functors v0.5.2 [34004b35] + HypergeometricFunctions v0.3.28 [92d709cd] + IrrationalConstants v0.2.4 [692b3bcd] + JLLWrappers v1.7.0 [ec8451be] + KernelFunctions v0.10.65 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.35 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.8.0 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.5 [4c63d2b9] + StatsFuns v1.5.0 [62fd8b95] + TensorCore v0.1.1 [700de1a5] + ZygoteRules v0.2.7 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown 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 v1.12.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [8e850b90] + libblastrampoline_jll v5.13.1+0 Installation completed after 7.37s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4647.3 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 25 already precompiled. Precompiling package dependencies... Precompilation completed after 982.92s ################################################################################ # Testing # Testing AbstractGPs Status `/tmp/jl_d7w8T2/Project.toml` [99985d1d] AbstractGPs v0.5.24 [4c88cf16] Aqua v0.8.13 [31c24e10] Distributions v0.25.120 [e30172f5] Documenter v1.14.1 [1a297f60] FillArrays v1.13.0 [26cc04aa] FiniteDifferences v0.12.32 [90014a1f] PDMats v0.11.35 [91a5bcdd] Plots v1.40.16 [10745b16] Statistics v1.11.1 ⌅ [e88e6eb3] Zygote v0.6.77 [37e2e46d] LinearAlgebra v1.12.0 [44cfe95a] Pkg v1.13.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_d7w8T2/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [621f4979] AbstractFFTs v1.5.0 [99985d1d] AbstractGPs v0.5.24 [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.3.0 [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.13 [a9b6321e] Atomix v1.1.1 [d1d4a3ce] BitFlags v0.1.9 [fa961155] CEnum v0.5.0 [082447d4] ChainRules v1.72.5 [d360d2e6] ChainRulesCore v1.25.2 [944b1d66] 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CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.11.1+1 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.5.20 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.1+0 [efcefdf7] PCRE2_jll v10.44.0+1 [bea87d4a] SuiteSparse_jll v7.8.3+2 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.64.0+1 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... [ Info: Ran util tests [ Info: Ran abstract_gp tests ┌ Warning: implicit `obsdim=2` argument is deprecated and now has to be passed explicitly to specify that each column corresponds to one observation │ caller = _pullback(::Zygote.Context{false}, ::typeof(Core.kwcall), ::@NamedTuple{obsdim::Nothing}, ::typeof(KernelFunctions.vec_of_vecs), ::Matrix{Float64}) at interface2.jl:0 └ @ Core ~/.julia/packages/Zygote/zowwZ/src/compiler/interface2.jl:0 [ Info: Ran gp tests ┌ Warning: `elbo(dtc::DTC, fx, y)` is deprecated, use `_warn_elbo_called_with_DTC(dtc, fx, y)` instead. │ caller = macro expansion at Test.jl:677 [inlined] └ @ Core /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:677 ┌ Warning: `elbo` was called with an object of type `DTC`, but should only be called with the `VFE` type instead └ @ AbstractGPs ~/.julia/packages/AbstractGPs/lWdNB/src/deprecations.jl:12 ┌ Warning: `elbo` was called with an object of type `DTC`, but should only be called with the `VFE` type instead └ @ AbstractGPs ~/.julia/packages/AbstractGPs/lWdNB/src/deprecations.jl:12 [ Info: Ran posterior_gp tests [ Info: Ran latent_gp tests [ Info: Ran deprecation tests ┌ Warning: Unable to determine HTML(edit_link = ...) from remote HEAD branch, defaulting to "master". │ Calling `git remote` failed with an exception. Set JULIA_DEBUG=Documenter to see the error. │ Unless this is due to a configuration error, the relevant variable should be set explicitly. └ @ Documenter ~/.julia/packages/Documenter/eoWm2/src/utilities/utilities.jl:665 [ Info: SetupBuildDirectory: setting up build directory. [ Info: Doctest: running doctests. [ Info: Skipped ExpandTemplates step (doctest only). [ Info: Skipped CrossReferences step (doctest only). [ Info: Skipped CheckDocument step (doctest only). [ Info: Skipped Populate step (doctest only). [ Info: Skipped RenderDocument step (doctest only). Activating project at `~/.julia/packages/AbstractGPs/lWdNB/test/ppl` Resolving package versions... Installed LRUCache ─────────────────── v1.6.2 Installed ConsoleProgressMonitor ───── v0.1.2 Installed AbstractMCMC ─────────────── v5.6.3 Installed FFTW ─────────────────────── v1.9.0 Installed OffsetArrays ─────────────── v1.17.0 Installed AxisArrays ───────────────── v0.4.7 Installed Accessors ────────────────── v0.1.42 Installed AdvancedPS ───────────────── v0.5.4 Installed ProgressMeter ────────────── v1.10.4 Installed EnumX ────────────────────── v1.0.5 Installed Roots ────────────────────── v2.2.8 Installed StatisticalTraits ────────── v3.5.0 Installed Optimisers ───────────────── v0.4.6 Installed NNlib ────────────────────── v0.9.30 Installed Turing ───────────────────── v0.30.9 Installed NaturalSort ──────────────── v1.0.0 Installed InitialValues ────────────── v0.3.1 Installed IntelOpenMP_jll ──────────── v2025.0.4+0 Installed FunctionWrappers ─────────── v1.1.3 Installed RecursiveArrayTools ──────── v3.34.1 Installed InvertedIndices ──────────── v1.3.1 Installed RandomNumbers ────────────── v1.6.0 Installed Bijectors ────────────────── v0.13.18 Installed LogDensityProblemsAD ─────── v1.9.0 Installed SimpleUnPack ─────────────── v1.1.0 Installed Functors ─────────────────── v0.4.12 Installed DefineSingletons ─────────── v0.1.2 Installed SciMLBase ────────────────── v2.103.0 Installed EllipticalSliceSampling ──── v2.0.0 Installed ADTypes ──────────────────── v0.2.7 Installed MicroCollections ─────────── v0.1.4 Installed Ratios ───────────────────── v0.4.5 Installed MappedArrays ─────────────── v0.4.2 Installed Random123 ────────────────── v1.7.1 Installed ExprTools ────────────────── v0.1.10 Installed Tracker ──────────────────── v0.2.38 Installed DynamicPPL ───────────────── v0.24.11 Installed LeftChildRightSiblingTrees ─ v0.2.0 Installed MCMCDiagnosticTools ──────── v0.3.14 Installed BangBang ─────────────────── v0.3.40 Installed ProgressLogging ──────────── v0.1.5 Installed MCMCChains ───────────────── v6.0.7 Installed SciMLStructures ──────────── v1.7.0 Installed FunctionWrappersWrappers ─── v0.1.3 Installed oneTBB_jll ───────────────── v2022.0.0+0 Installed ArgCheck ─────────────────── v2.5.0 Installed NamedArrays ──────────────── v0.10.4 Installed PrettyTables ─────────────── v2.4.0 Installed AbstractPPL ──────────────── v0.7.1 Installed SciMLOperators ───────────── v1.3.1 Installed Setfield ─────────────────── v1.1.2 Installed DistributionsAD ──────────── v0.6.58 Installed MKL_jll ──────────────────── v2025.0.1+1 Installed Libtask ──────────────────── v0.8.8 Installed AdvancedVI ───────────────── v0.2.12 Installed ExproniconLite ───────────── v0.10.14 Installed KernelDensity ────────────── v0.6.10 Installed InplaceOps ───────────────── v0.3.0 Installed Combinatorics ────────────── v1.0.3 Installed ArrayInterface ───────────── v7.19.0 Installed AdvancedMH ───────────────── v0.8.8 Installed Interpolations ───────────── v0.16.1 Installed RangeArrays ──────────────── v0.3.2 Installed FFTW_jll ─────────────────── v3.3.11+0 Installed CommonSolve ──────────────── v0.2.4 Installed InverseFunctions ─────────── v0.1.17 Installed ScientificTypesBase ──────── v3.0.0 Installed Crayons ──────────────────── v4.1.1 Installed IntervalSets ─────────────── v0.7.11 Installed IterTools ────────────────── v1.10.0 Installed RuntimeGeneratedFunctions ── v0.5.15 Installed Jieko ────────────────────── v0.2.1 Installed Baselet ──────────────────── v0.1.1 Installed MLJModelInterface ────────── v1.11.1 Installed Transducers ──────────────── v0.4.80 Installed TerminalLoggers ──────────── v0.1.7 Installed AdvancedHMC ──────────────── v0.6.4 Installed Moshi ────────────────────── v0.3.7 Installed AxisAlgorithms ───────────── v1.1.0 Installed SymbolicIndexingInterface ── v0.3.41 Installed WoodburyMatrices ─────────── v1.0.0 Installed SplittablesBase ──────────── v0.1.15 Installed StringManipulation ───────── v0.4.1 Installed StructArrays ─────────────── v0.6.21 Installed LogDensityProblems ───────── v2.1.2 Installed ForwardDiff ──────────────── v0.10.38 Installed DensityInterface ─────────── v0.4.0 Installed ChangesOfVariables ───────── v0.1.10 Installing 2 artifacts Installed artifact oneTBB 435.6 KiB Installed artifact FFTW 2.2 MiB AbstractGPs: Error During Test at /home/pkgeval/.julia/packages/AbstractGPs/lWdNB/test/runtests.jl:41 Got exception outside of a @test SystemError: opening file "/home/pkgeval/.julia/packages/AbstractGPs/lWdNB/test/ppl/Project.toml": Permission denied Stacktrace: [1] systemerror(p::String, errno::Int32; extrainfo::Nothing) @ Base ./error.jl:186 [2] open(fname::String; lock::Bool, read::Nothing, write::Nothing, create::Nothing, truncate::Bool, append::Nothing) @ Base ./iostream.jl:317 [3] open @ ./iostream.jl:296 [inlined] [4] open(fname::String, mode::String; lock::Bool) @ Base ./iostream.jl:380 [5] open(fname::String, mode::String) @ Base ./iostream.jl:379 [6] open(::Base.var"#write##0#write##1"{String, Tuple{}}, ::String, ::Vararg{String}; kwargs::@Kwargs{}) @ Base ./io.jl:408 [7] open @ ./io.jl:407 [inlined] [8] write @ ./io.jl:489 [inlined] [9] write_project @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/project.jl:315 [inlined] [10] write_project @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/project.jl:296 [inlined] [11] write_project(env::Pkg.Types.EnvCache) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/Pkg/src/project.jl:294 [12] write_env(env::Pkg.Types.EnvCache; update_undo::Bool, skip_writing_project::Bool) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Types.jl:1259 [13] write_env @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Types.jl:1225 [inlined] [14] develop(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}, new_git::Set{Base.UUID}; preserve::PreserveLevel, platform::Base.BinaryPlatforms.Platform) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:1785 [15] develop @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:1771 [inlined] [16] develop(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; shared::Bool, preserve::PreserveLevel, platform::Base.BinaryPlatforms.Platform, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:285 [17] develop(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:164 [18] develop(pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:153 [19] develop(pkg::PackageSpec) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:151 [20] top-level scope @ ~/.julia/packages/AbstractGPs/lWdNB/test/runtests.jl:42 [21] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [22] macro expansion @ ~/.julia/packages/AbstractGPs/lWdNB/test/runtests.jl:97 [inlined] [23] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [24] top-level scope @ none:6 [25] eval(m::Module, e::Any) @ Core ./boot.jl:489 [26] exec_options(opts::Base.JLOptions) @ Base ./client.jl:287 [27] _start() @ Base ./client.jl:554 Test Summary: | Pass Error Total Time AbstractGPs | 791 1 792 10m33.8s Code quality (Aqua.jl) | 11 11 1m17.4s util | 87 87 2m23.2s abstract_gp | 359 359 2m44.8s gp | 102 102 1m36.0s posterior_gp | 217 217 1m05.3s latent_gp | 8 8 0.9s deprecations | 6 6 0.6s doctests | 1 1 1m02.2s RNG of the outermost testset: Xoshiro(0x23fe44cfe46cff96, 0x5450a41716481abb, 0x975f73fc90bbff56, 0xdd80a2a6c43abc6c, 0x2451e793588c7369) ERROR: LoadError: Some tests did not pass: 791 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/AbstractGPs/lWdNB/test/runtests.jl:41 Testing failed after 697.04s ERROR: LoadError: Package AbstractGPs errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/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/v1.12/Pkg/src/Operations.jl:2458 [3] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2313 [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/v1.12/Pkg/src/API.jl:511 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:164 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 [7] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:151 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [10] include(mod::Module, _path::String) @ Base ./Base.jl:305 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:321 [12] _start() @ Base ./client.jl:554 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1756.39s: package tests unexpectedly errored