Package evaluation of Diversity on Julia 1.12.0-rc1.2 (995ff9db19*) started at 2025-07-14T14:30:32.298 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.9s ################################################################################ # Installation # Installing Diversity... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [d3d5718d] + Diversity v0.5.15 Updating `~/.julia/environments/v1.12/Manifest.toml` [34da2185] + Compat v4.17.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [d3d5718d] + Diversity v0.5.15 [a58aae7d] + EcoBase v0.1.7 [842dd82b] + InlineStrings v1.4.4 [41ab1584] + InvertedIndices v1.3.1 [82899510] + IteratorInterfaceExtensions v1.0.0 [b964fa9f] + LaTeXStrings v1.4.0 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [91c51154] + SentinelArrays v1.4.8 [a2af1166] + SortingAlgorithms v1.2.1 [10745b16] + Statistics v1.11.1 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [d6f4376e] + Markdown v1.11.0 [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 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [8e850b90] + libblastrampoline_jll v5.13.1+0 Installation completed after 3.56s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... ERROR: LoadError: The following 1 direct dependency failed to precompile: SpatialEcology Failed to precompile SpatialEcology [348f2d5d-71a3-5ad4-b565-8af070f99681] to "/home/pkgeval/.julia/compiled/v1.12/SpatialEcology/jl_URysi0". WARNING: Imported binding DataFrames.aggregate was undeclared at import time during import to SpatialEcology. ERROR: LoadError: invalid method definition in SpatialEcology: exported function DataFrames.aggregate does not exist Stacktrace: [1] top-level scope @ ~/.julia/packages/SpatialEcology/2IBpN/src/Operations.jl:4 [2] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [3] top-level scope @ ~/.julia/packages/SpatialEcology/2IBpN/src/SpatialEcology.jl:53 [4] include(mod::Module, _path::String) @ Base ./Base.jl:305 [5] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing) @ Base ./loading.jl:2991 [6] top-level scope @ stdin:5 [7] eval(m::Module, e::Any) @ Core ./boot.jl:489 [8] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2837 [9] include_string @ ./loading.jl:2847 [inlined] [10] exec_options(opts::Base.JLOptions) @ Base ./client.jl:319 [11] _start() @ Base ./client.jl:554 in expression starting at /home/pkgeval/.julia/packages/SpatialEcology/2IBpN/src/Operations.jl:4 in expression starting at /home/pkgeval/.julia/packages/SpatialEcology/2IBpN/src/SpatialEcology.jl:2 in expression starting at stdin: in expression starting at /PkgEval.jl/scripts/precompile.jl:37 Precompilation failed after 732.02s ################################################################################ # Testing # Testing Diversity Status `/tmp/jl_dHx7OJ/Project.toml` [39de3d68] AxisArrays v0.4.7 [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.7.0 [b4f34e82] Distances v0.10.12 [d3d5718d] Diversity v0.5.15 [a58aae7d] EcoBase v0.1.7 [d7ba0133] Git v1.4.0 ⌅ [98e50ef6] JuliaFormatter v1.0.62 [e1d29d7a] Missings v1.2.0 [aea672f4] Phylo v0.5.4 [6f49c342] RCall v0.14.8 [3cdcf5f2] RecipesBase v1.3.4 [58378933] ResearchSoftwareMetadata v0.1.5 [348f2d5d] SpatialEcology v0.9.16 [10745b16] Statistics v1.11.1 [2913bbd2] StatsBase v0.34.5 [b77e0a4c] InteractiveUtils v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [56ddb016] Logging v1.11.0 [44cfe95a] Pkg v1.13.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_dHx7OJ/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [ec485272] ArnoldiMethod v0.4.0 [15f4f7f2] AutoHashEquals v2.2.0 [39de3d68] AxisArrays v0.4.7 [d1d4a3ce] BitFlags v0.1.9 [00ebfdb7] CSTParser v3.4.3 [336ed68f] CSV v0.10.15 [324d7699] CategoricalArrays v0.10.8 ⌅ [8be319e6] Chain v0.5.0 [944b1d66] CodecZlib v0.7.8 ⌅ [a80b9123] CommonMark v0.8.16 [34da2185] Compat v4.17.0 [f0e56b4a] ConcurrentUtilities v2.5.0 [8f4d0f93] Conda v1.10.2 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 ⌅ [1313f7d8] DataFramesMeta v0.14.1 [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [e7dc6d0d] DataValues v0.4.13 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.120 [d3d5718d] Diversity v0.5.15 [ffbed154] DocStringExtensions v0.9.5 [a58aae7d] EcoBase v0.1.7 [460bff9d] ExceptionUnwrapping v0.1.11 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.13.0 [d7ba0133] Git v1.4.0 [c27321d9] Glob v1.3.1 [86223c79] Graphs v1.13.0 [cd3eb016] HTTP v1.10.17 [34004b35] HypergeometricFunctions v0.3.28 [d25df0c9] Inflate v0.1.5 [842dd82b] InlineStrings v1.4.4 [8197267c] IntervalSets v0.7.11 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [c8e1da08] IterTools v1.10.0 [1c8ee90f] IterableTables v1.0.0 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 ⌅ [98e50ef6] JuliaFormatter v1.0.62 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [e6f89c97] LoggingExtras v1.1.0 [1914dd2f] MacroTools v0.5.16 [739be429] MbedTLS v1.1.9 [e1d29d7a] Missings v1.2.0 [4d8831e6] OpenSSL v1.5.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.35 [fae87a5f] ParserCombinator v2.2.1 [69de0a69] Parsers v2.8.3 [aea672f4] Phylo v0.5.4 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [6f49c342] RCall v0.14.8 [9ae346a0] RandomBooleanMatrices v0.1.2 [e6cf234a] RandomNumbers v1.6.0 [b3c3ace0] RangeArrays v0.3.2 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [58378933] ResearchSoftwareMetadata v0.1.5 [79098fc4] Rmath v0.8.0 [91c51154] SentinelArrays v1.4.8 [1277b4bf] ShiftedArrays v2.0.0 [777ac1f9] SimpleBufferStream v1.2.0 [699a6c99] SimpleTraits v0.9.4 [a2af1166] SortingAlgorithms v1.2.1 [348f2d5d] SpatialEcology v0.9.16 [276daf66] SpecialFunctions v2.5.1 [90137ffa] StaticArrays v1.9.13 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.5 [4c63d2b9] StatsFuns v1.5.0 [3eaba693] StatsModels v0.7.4 [69024149] StringEncodings v0.3.7 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [382cd787] TableTraitsUtils v1.0.2 [bd369af6] Tables v1.12.1 [0796e94c] Tokenize v0.5.29 [3bb67fe8] TranscodingStreams v0.11.3 [5c2747f8] URIs v1.6.1 [1986cc42] Unitful v1.23.1 [81def892] VersionParsing v1.3.0 [ea10d353] WeakRefStrings v1.4.2 [1b915085] WinReg v1.0.0 [76eceee3] WorkerUtilities v1.6.1 [ddb6d928] YAML v0.4.14 [2e619515] Expat_jll v2.6.5+0 [f8c6e375] Git_jll v2.50.0+0 [94ce4f54] Libiconv_jll v1.18.0+0 [c8ffd9c3] MbedTLS_jll v2.28.6+2 [9bd350c2] OpenSSH_jll v10.0.1+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [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 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [1a1011a3] SharedArrays v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.12.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [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 v8.11.1+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: Running tests for files: = API.jl = Diversity.jl = DiversityMeasure.jl = EcoBase.jl = Ecology.jl = EffectiveNumbers.jl = GeneralisedDiversities.jl = Hill.jl = Interface.jl = Iterators.jl = Jost.jl = Metacommunity.jl = Partition.jl = Types.jl [ Info: Running tests... * Testing API.jl ... * Testing Diversity.jl ... * Testing DiversityMeasure.jl ... * Testing EcoBase.jl ... Precompiling packages... 3111.4 ms ✓ RandomBooleanMatrices 9168.9 ms ✓ DataFramesMeta Info Given SpatialEcology was explicitly requested, output will be shown live  WARNING: Imported binding DataFrames.aggregate was undeclared at import time during import to SpatialEcology. ERROR: LoadError: invalid method definition in SpatialEcology: exported function DataFrames.aggregate does not exist Stacktrace:  [1] top-level scope  @ ~/.julia/packages/SpatialEcology/2IBpN/src/Operations.jl:4  [2] include(mapexpr::Function, mod::Module, _path::String)  @ Base ./Base.jl:306  [3] top-level scope  @ ~/.julia/packages/SpatialEcology/2IBpN/src/SpatialEcology.jl:53  [4] include(mod::Module, _path::String)  @ Base ./Base.jl:305  [5] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:2991  [6] top-level scope  @ stdin:5  [7] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [8] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:2837  [9] include_string  @ ./loading.jl:2847 [inlined]  [10] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:319  [11] _start()  @ Base ./client.jl:554 in expression starting at /home/pkgeval/.julia/packages/SpatialEcology/2IBpN/src/Operations.jl:4 in expression starting at /home/pkgeval/.julia/packages/SpatialEcology/2IBpN/src/SpatialEcology.jl:2 in expression starting at stdin:5 ✗ SpatialEcology 2 dependencies successfully precompiled in 25 seconds. 53 already precompiled. t = EcoBase: Error During Test at /home/pkgeval/.julia/packages/Diversity/trAoz/test/runtests.jl:94 Got exception outside of a @test LoadError: The following 1 direct dependency failed to precompile: SpatialEcology Failed to precompile SpatialEcology [348f2d5d-71a3-5ad4-b565-8af070f99681] to "/home/pkgeval/.julia/compiled/v1.12/SpatialEcology/jl_VqmDGf". WARNING: Imported binding DataFrames.aggregate was undeclared at import time during import to SpatialEcology. ERROR: LoadError: invalid method definition in SpatialEcology: exported function DataFrames.aggregate does not exist Stacktrace: [1] top-level scope @ ~/.julia/packages/SpatialEcology/2IBpN/src/Operations.jl:4 [2] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [3] top-level scope @ ~/.julia/packages/SpatialEcology/2IBpN/src/SpatialEcology.jl:53 [4] include(mod::Module, _path::String) @ Base ./Base.jl:305 [5] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing) @ Base ./loading.jl:2991 [6] top-level scope @ stdin:5 [7] eval(m::Module, e::Any) @ Core ./boot.jl:489 [8] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2837 [9] include_string @ ./loading.jl:2847 [inlined] [10] exec_options(opts::Base.JLOptions) @ Base ./client.jl:319 [11] _start() @ Base ./client.jl:554 in expression starting at /home/pkgeval/.julia/packages/SpatialEcology/2IBpN/src/Operations.jl:4 in expression starting at /home/pkgeval/.julia/packages/SpatialEcology/2IBpN/src/SpatialEcology.jl:2 in expression starting at stdin: in expression starting at /home/pkgeval/.julia/packages/Diversity/trAoz/test/test_EcoBase.jl:3 * Testing Ecology.jl ... * Testing EffectiveNumbers.jl ... * Testing GeneralisedDiversities.jl ... * Testing Hill.jl ... ┌ Warning: Abundances not normalised to 1, correcting... └ @ Diversity ~/.julia/packages/Diversity/trAoz/src/Metacommunity.jl:124 * Testing Interface.jl ... * Testing Iterators.jl ... Precompiling packages... 5816.1 ms ✓ Diversity → DiversityAxisArraysExt 1 dependency successfully precompiled in 6 seconds. 45 already precompiled. Precompiling packages... 4025.6 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 5 seconds. 50 already precompiled. * Testing Jost.jl ... * Testing Metacommunity.jl ... ┌ Warning: Abundances not normalised to 1, correcting... └ @ Diversity ~/.julia/packages/Diversity/trAoz/src/Metacommunity.jl:74 * Testing Partition.jl ... * Testing Types.jl ... [ Info: Running tests for extensions: = DiversityAxisArraysExt.jl = DiversityPhyloExt.jl [ Info: Running extension tests... * Testing DiversityAxisArraysExt.jl extension... * Testing DiversityPhyloExt.jl extension... Test Summary: | Pass Error Broken Total Time Diversity.jl | 258 1 2 261 4m13.3s t = API | 2 2 1.5s t = Diversity | 0 0.0s t = DiversityMeasure | 67 67 1m05.1s t = EcoBase | 1 1 25.8s t = Ecology | 42 2 44 28.0s t = EffectiveNumbers | 41 41 8.5s t = GeneralisedDiversities | 16 16 2.7s t = Hill | 9 9 5.0s t = Interface | 1 1 0.8s t = Iterators | 16 16 43.3s t = Jost | 9 9 45.7s t = Metacommunity | 16 16 7.8s t = Partition | 5 5 0.2s t = Types | 16 16 6.7s t = DiversityAxisArraysExt | 3 3 1.8s t = DiversityPhyloExt | 14 14 8.3s RNG of the outermost testset: Xoshiro(0x9951797c85a704f1, 0xb9d66be14dfba82b, 0xb170153285fd9556, 0xe90a07f7bdd1fd77, 0x9d4b5ee33e4bd661) ERROR: LoadError: Some tests did not pass: 258 passed, 0 failed, 1 errored, 2 broken. in expression starting at /home/pkgeval/.julia/packages/Diversity/trAoz/test/runtests.jl:10 Testing failed after 281.43s ERROR: LoadError: Package Diversity 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 1073.11s: package fails to precompile