Package evaluation of AbstractGPs on Julia 1.13.0-DEV.640 (0a970d81aa*) started at 2025-05-27T17:13:00.705 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.09s ################################################################################ # Installation # Installing AbstractGPs... Resolving package versions... Installed Rmath_jll ─────────────── v0.5.1+0 Installed ConstructionBase ──────── v1.5.8 Installed CompositionsBase ──────── v0.1.2 Installed MacroTools ────────────── v0.5.16 Installed FillArrays ────────────── v1.13.0 Installed DataStructures ────────── v0.18.22 Installed HypergeometricFunctions ─ v0.3.28 Installed AliasTables ───────────── v1.1.3 Installed RecipesBase ───────────── v1.3.4 Installed OrderedCollections ────── v1.8.1 Installed Functors ──────────────── v0.5.2 Installed DataAPI ───────────────── v1.16.0 Installed Compat ────────────────── v4.16.0 Installed Statistics ────────────── v1.11.1 Installed StatsBase ─────────────── v0.34.5 Installed TensorCore ────────────── v0.1.1 Installed StatsAPI ──────────────── v1.7.0 Installed IrrationalConstants ───── v0.2.4 Installed Distances ─────────────── v0.10.12 Installed Requires ──────────────── v1.3.1 Installed PrecompileTools ───────── v1.3.2 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed Rmath ─────────────────── v0.8.0 Installed QuadGK ────────────────── v2.11.2 Installed LogExpFunctions ───────── v0.3.29 Installed ChainRulesCore ────────── v1.25.1 Installed Reexport ──────────────── v1.2.2 Installed PtrArrays ─────────────── v1.3.0 Installed StatsFuns ─────────────── v1.5.0 Installed SpecialFunctions ──────── v2.5.1 Installed Preferences ───────────── v1.4.3 Installed AbstractGPs ───────────── v0.5.24 Installed KernelFunctions ───────── v0.10.65 Installed Distributions ─────────── v0.25.120 Installed Missings ──────────────── v1.2.0 Installed ZygoteRules ───────────── v0.2.7 Installed JLLWrappers ───────────── v1.7.0 Installed DocStringExtensions ───── v0.9.4 Installed SortingAlgorithms ─────── v1.2.1 Installed PDMats ────────────────── v0.11.35 Installing 2 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Rmath 121.9 KiB Updating `~/.julia/environments/v1.13/Project.toml` [99985d1d] + AbstractGPs v0.5.24 Updating `~/.julia/environments/v1.13/Manifest.toml` [99985d1d] + AbstractGPs v0.5.24 [66dad0bd] + AliasTables v1.1.3 [d360d2e6] + ChainRulesCore v1.25.1 [34da2185] + Compat v4.16.0 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.5.8 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.4 [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 v1.7.0 [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 v7.10.1+0 [8e850b90] + libblastrampoline_jll v5.12.0+0 Installation completed after 7.21s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4468.0 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 25 already precompiled. Precompiling package dependencies... Precompilation completed after 924.95s ################################################################################ # Testing # Testing AbstractGPs Status `/tmp/jl_UEeKUj/Project.toml` [99985d1d] AbstractGPs v0.5.24 [4c88cf16] Aqua v0.8.12 [31c24e10] Distributions v0.25.120 [e30172f5] Documenter v1.11.4 [1a297f60] FillArrays v1.13.0 [26cc04aa] FiniteDifferences v0.12.32 [90014a1f] PDMats v0.11.35 [91a5bcdd] Plots v1.40.13 [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_UEeKUj/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 v0.8.12 [a9b6321e] Atomix v1.1.1 [d1d4a3ce] BitFlags v0.1.9 [fa961155] CEnum v0.5.0 [082447d4] ChainRules v1.72.3 [d360d2e6] ChainRulesCore v1.25.1 [944b1d66] 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v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.12.1+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 v3.5.0+0 [efcefdf7] PCRE2_jll v10.44.0+1 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.12.0+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+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... WARNING: Detected access to binding `KernelFunctions.kernelpdmat` in a world prior to its definition world. Julia 1.12 has introduced more strict world age semantics for global bindings. !!! This code may malfunction under Revise. !!! This code will error in future versions of Julia. Hint: Add an appropriate `invokelatest` around the access to this binding. To make this warning an error, and hence obtain a stack trace, use `julia --depwarn=error`. [ 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:727 [inlined] └ @ Core /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:727 ┌ 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/iRt2s/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 DefineSingletons ─────────── v0.1.2 Installed MKL_jll ──────────────────── v2025.0.1+1 Installed AbstractPPL ──────────────── v0.7.1 Installed ArgCheck ─────────────────── v2.5.0 Installed DistributionsAD ──────────── v0.6.58 Installed InitialValues ────────────── v0.3.1 Installed Functors ─────────────────── v0.4.12 Installed Turing ───────────────────── v0.30.9 Installed EnumX ────────────────────── v1.0.5 Installed WoodburyMatrices ─────────── v1.0.0 Installed InverseFunctions ─────────── v0.1.17 Installed Jieko ────────────────────── v0.2.1 Installed MappedArrays ─────────────── v0.4.2 Installed Crayons ──────────────────── v4.1.1 Installed MCMCChains ───────────────── v6.0.7 Installed RecursiveArrayTools ──────── v3.33.0 Installed RangeArrays ──────────────── v0.3.2 Installed oneTBB_jll ───────────────── v2022.0.0+0 Installed ADTypes ──────────────────── v0.2.7 Installed NaturalSort ──────────────── v1.0.0 Installed DensityInterface ─────────── v0.4.0 Installed ExprTools ────────────────── v0.1.10 Installed ConsoleProgressMonitor ───── v0.1.2 Installed ArrayInterface ───────────── v7.19.0 Installed Optimisers ───────────────── v0.4.6 Installed IntelOpenMP_jll ──────────── v2025.0.4+0 Installed TerminalLoggers ──────────── v0.1.7 Installed MCMCDiagnosticTools ──────── v0.3.14 Installed AdvancedMH ───────────────── v0.8.7 Installed Roots ────────────────────── v2.2.7 Installed LeftChildRightSiblingTrees ─ v0.2.0 Installed DynamicPPL ───────────────── v0.24.11 Installed RandomNumbers ────────────── v1.6.0 Installed Setfield ─────────────────── v1.1.2 Installed SplittablesBase ──────────── v0.1.15 Installed Baselet ──────────────────── v0.1.1 Installed LRUCache ─────────────────── v1.6.2 Installed Interpolations ───────────── v0.15.1 Installed NamedArrays ──────────────── v0.10.3 Installed Transducers ──────────────── v0.4.80 Installed AxisArrays ───────────────── v0.4.7 Installed AdvancedVI ───────────────── v0.2.11 Installed SimpleUnPack ─────────────── v1.1.0 Installed CommonSolve ──────────────── v0.2.4 Installed ForwardDiff ──────────────── v0.10.38 Installed AdvancedPS ───────────────── v0.5.4 Installed Moshi ────────────────────── v0.3.5 Installed KernelDensity ────────────── v0.6.9 Installed Combinatorics ────────────── v1.0.3 Installed FunctionWrappersWrappers ─── v0.1.3 Installed InplaceOps ───────────────── v0.3.0 Installed InvertedIndices ──────────── v1.3.1 Installed SciMLStructures ──────────── v1.7.0 Installed SciMLOperators ───────────── v1.3.0 Installed BangBang ─────────────────── v0.3.40 Installed NNlib ────────────────────── v0.9.30 Installed AxisAlgorithms ───────────── v1.1.0 Installed LogDensityProblemsAD ─────── v1.9.0 Installed FunctionWrappers ─────────── v1.1.3 Installed StringManipulation ───────── v0.4.1 Installed Libtask ──────────────────── v0.8.8 Installed StatisticalTraits ────────── v3.4.0 Installed IterTools ────────────────── v1.10.0 Installed SciMLBase ────────────────── v2.95.0 Installed Accessors ────────────────── v0.1.42 Installed Bijectors ────────────────── v0.13.18 Installed PrettyTables ─────────────── v2.4.0 Installed AdvancedHMC ──────────────── v0.6.4 Installed MicroCollections ─────────── v0.1.4 Installed RuntimeGeneratedFunctions ── v0.5.14 Installed ProgressLogging ──────────── v0.1.4 Installed Random123 ────────────────── v1.7.1 Installed StructArrays ─────────────── v0.6.21 Installed SymbolicIndexingInterface ── v0.3.40 Installed OffsetArrays ─────────────── v1.17.0 Installed ExproniconLite ───────────── v0.10.14 Installed LogDensityProblems ───────── v2.1.2 Installed ProgressMeter ────────────── v1.10.4 Installed ScientificTypesBase ──────── v3.0.0 Installed Ratios ───────────────────── v0.4.5 Installed Tracker ──────────────────── v0.2.38 Installed EllipticalSliceSampling ──── v2.0.0 Installed AbstractMCMC ─────────────── v5.6.2 Installed IntervalSets ─────────────── v0.7.11 Installed FFTW_jll ─────────────────── v3.3.11+0 Installed FFTW ─────────────────────── v1.8.1 Installed MLJModelInterface ────────── v1.11.1 Installed ChangesOfVariables ───────── v0.1.10 Installing 2 artifacts Installed artifact FFTW 2.2 MiB Installed artifact oneTBB 435.6 KiB 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#330 @ ./io.jl:408 [7] open @ ./io.jl:407 [inlined] [8] write @ ./io.jl:489 [inlined] [9] write_project(project::Dict{String, Any}, project_file::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/Pkg/src/project.jl:301 [10] write_project @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/project.jl:282 [inlined] [11] write_project @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/project.jl:280 [inlined] [12] write_env(env::Pkg.Types.EnvCache; update_undo::Bool, skip_writing_project::Bool) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Types.jl:1249 [13] write_env @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Types.jl:1220 [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/v1.13/Pkg/src/Operations.jl:1759 [15] develop @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:1745 [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/v1.13/Pkg/src/API.jl:274 [17] develop(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:164 [18] develop(pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:153 [19] develop(pkg::PackageSpec) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/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/v1.13/Test/src/Test.jl:1833 [inlined] [22] macro expansion @ ~/.julia/packages/AbstractGPs/lWdNB/test/runtests.jl:97 [inlined] [23] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [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:297 [27] _start() @ Base ./client.jl:564 Test Summary: | Pass Error Total Time AbstractGPs | 791 1 792 10m25.6s Code quality (Aqua.jl) | 11 11 1m21.0s util | 87 87 2m11.5s abstract_gp | 359 359 2m37.1s gp | 102 102 1m31.6s posterior_gp | 217 217 1m02.8s latent_gp | 8 8 0.7s deprecations | 6 6 0.9s doctests | 1 1 1m16.5s RNG of the outermost testset: Xoshiro(0xac5433ef76a5eb55, 0xd536cb8bbb5416c1, 0xb686a7df5cf76a2a, 0xcb9c70b678da42d1, 0x4de0f2ecc76f1621) 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 685.39s ERROR: LoadError: Package AbstractGPs 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:2421 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2276 [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:498 [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:164 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [7] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.13/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:309 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:331 [12] _start() @ Base ./client.jl:564 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1669.31s: package tests unexpectedly errored