Package evaluation to test Diversity on Julia 1.14.0-DEV.1711 (41ad7d9eeb*) started at 2026-02-12T16:00:49.236 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 12.42s ################################################################################ # Installation # Installing Diversity... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [d3d5718d] + Diversity v0.5.15 Updating `~/.julia/environments/v1.14/Manifest.toml` [34da2185] + Compat v4.18.1 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 [864edb3b] + DataStructures v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 [d3d5718d] + Diversity v0.5.15 [a58aae7d] + EcoBase v0.1.7 [842dd82b] + InlineStrings v1.4.5 [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 v1.3.3 [21216c6a] + Preferences v1.5.1 [08abe8d2] + PrettyTables v3.1.2 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [91c51154] + SentinelArrays v1.4.9 [a2af1166] + SortingAlgorithms v1.2.2 [10745b16] + Statistics v1.11.1 [892a3eda] + StringManipulation v0.4.2 [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 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [d6f4376e] + Markdown v1.11.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [6462fe0b] + Sockets v1.11.0 [f489334b] + StyledStrings v1.13.0 [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 v0.3.30+0 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 4.67s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ TestEnv ~/.julia/packages/TestEnv/B6c9D/src/julia-1.13/activate_set.jl:78 Precompiling package dependencies... Precompiling packages... 2143.5 ms ✓ DataValues 2349.9 ms ✓ TableMetadataTools 2967.2 ms ✓ QuadGK 2865.6 ms ✓ RandomBooleanMatrices 2237.5 ms ✓ PDMats → StatsBaseExt 2889.1 ms ✓ CategoricalArrays → CategoricalArraysStatsBaseExt 1485.8 ms ✓ EcoBase 1572.7 ms ✓ CategoricalArrays → CategoricalArraysRecipesBaseExt 86268.4 ms ✓ DataFrames 41738.5 ms ✓ JuliaFormatter 22918.1 ms ✓ CSV 1256.2 ms ✓ CategoricalArrays → CategoricalArraysJSONExt 3865.3 ms ✓ ResearchSoftwareMetadata 4971.2 ms ✓ StatsModels 1169.3 ms ✓ TableTraitsUtils 11478.2 ms ✓ Distributions 9492.1 ms ✓ Diversity 11136.5 ms ✓ DataFramesMeta 12069.8 ms ✓ RCall 1282.2 ms ✓ IterableTables 4015.8 ms ✓ Distributions → DistributionsTestExt 7711.5 ms ✓ Diversity → DiversityAxisArraysExt 13344.8 ms ✓ SpatialEcology 11820.4 ms ✓ RCall → RCallAxisArraysExt 19574.8 ms ✓ Phylo 17368.5 ms ✓ Phylo → PhyloRCallExt 14350.8 ms ✓ Diversity → DiversityPhyloExt 27 dependencies successfully precompiled in 319 seconds. 147 already precompiled. Precompilation completed after 413.11s ################################################################################ # Testing # Testing Diversity Test Could not use exact versions of packages in manifest, re-resolving. Note: if you do not check your manifest file into source control, then you can probably ignore this message. However, if you do check your manifest file into source control, then you probably want to pass the `allow_reresolve = false` kwarg when calling the `Pkg.test` function. Updating `/tmp/jl_FZFtDf/Project.toml` [39de3d68] + AxisArrays v0.4.8 [336ed68f] + CSV v0.10.15 [b4f34e82] + Distances v0.10.12 [d3d5718d] + Diversity v0.5.15 [d7ba0133] + Git v1.5.0 ⌅ [98e50ef6] + JuliaFormatter v1.0.62 [aea672f4] + Phylo v0.5.4 [6f49c342] + RCall v0.14.12 [58378933] + ResearchSoftwareMetadata v0.1.5 [348f2d5d] + SpatialEcology v0.9.17 [2913bbd2] + StatsBase v0.34.10 [56ddb016] ~ Logging ⇒ v1.11.0 [44cfe95a] ~ Pkg ⇒ v1.14.0 [8dfed614] ~ Test ⇒ v1.11.0 Updating `/tmp/jl_FZFtDf/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [ec485272] + ArnoldiMethod v0.4.0 [15f4f7f2] + AutoHashEquals v2.2.0 [39de3d68] + AxisArrays v0.4.8 [d1d4a3ce] + BitFlags v0.1.9 [00ebfdb7] + CSTParser v3.4.3 [336ed68f] + CSV v0.10.15 [324d7699] + CategoricalArrays v1.0.2 [8be319e6] + Chain v1.0.0 [944b1d66] + CodecZlib v0.7.8 ⌅ [a80b9123] + CommonMark v0.8.16 [f0e56b4a] + ConcurrentUtilities v2.5.0 [8f4d0f93] + Conda v1.10.3 [1313f7d8] + DataFramesMeta v0.15.6 ⌅ [864edb3b] ↓ DataStructures v0.19.3 ⇒ v0.18.22 [e7dc6d0d] + DataValues v0.4.13 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.123 [d3d5718d] + Diversity v0.5.15 [ffbed154] + DocStringExtensions v0.9.5 [460bff9d] + ExceptionUnwrapping v0.1.11 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.16.0 [d7ba0133] + Git v1.5.0 [c27321d9] + Glob v1.4.0 ⌃ [86223c79] + Graphs v1.13.1 [cd3eb016] + HTTP v1.10.19 [34004b35] + HypergeometricFunctions v0.3.28 [d25df0c9] + Inflate v0.1.5 [8197267c] + IntervalSets v0.7.13 [92d709cd] + IrrationalConstants v0.2.6 [c8e1da08] + IterTools v1.10.0 [1c8ee90f] + IterableTables v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 ⌅ [682c06a0] + JSON v0.21.4 ⌅ [98e50ef6] + JuliaFormatter v1.0.62 [2ab3a3ac] + LogExpFunctions v0.3.29 [e6f89c97] + LoggingExtras v1.2.0 [1914dd2f] + MacroTools v0.5.16 [739be429] + MbedTLS v1.1.9 [4d8831e6] + OpenSSL v1.6.1 [90014a1f] + PDMats v0.11.37 [fae87a5f] + ParserCombinator v2.2.1 [69de0a69] + Parsers v2.8.3 [aea672f4] + Phylo v0.5.4 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [6f49c342] + RCall v0.14.12 [9ae346a0] + RandomBooleanMatrices v0.1.2 [e6cf234a] + RandomNumbers v1.6.0 [b3c3ace0] + RangeArrays v0.3.2 [ae029012] + Requires v1.3.1 [58378933] + ResearchSoftwareMetadata v0.1.5 [79098fc4] + Rmath v0.9.0 [1277b4bf] + ShiftedArrays v2.0.0 [777ac1f9] + SimpleBufferStream v1.2.0 [699a6c99] + SimpleTraits v0.9.5 [348f2d5d] + SpatialEcology v0.9.17 [276daf66] + SpecialFunctions v2.7.1 [90137ffa] + StaticArrays v1.9.16 [1e83bf80] + StaticArraysCore v1.4.4 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [4c63d2b9] + StatsFuns v1.5.2 [3eaba693] + StatsModels v0.7.8 [69024149] + StringEncodings v0.3.7 [9ce81f87] + TableMetadataTools v0.1.0 [382cd787] + TableTraitsUtils v1.0.2 [0796e94c] + Tokenize v0.5.29 [3bb67fe8] + TranscodingStreams v0.11.3 [5c2747f8] + URIs v1.6.1 [1986cc42] + Unitful v1.28.0 [81def892] + VersionParsing v1.3.0 [ea10d353] + WeakRefStrings v1.4.2 [1b915085] + WinReg v1.0.0 [76eceee3] + WorkerUtilities v1.6.1 [ddb6d928] + YAML v0.4.16 [2e619515] + Expat_jll v2.7.3+0 [020c3dae] + Git_LFS_jll v3.7.0+0 [f8c6e375] + Git_jll v2.53.0+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [c8ffd9c3] + MbedTLS_jll v2.28.1010+0 [9bd350c2] + OpenSSH_jll v10.2.1+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [0dad84c5] + ArgTools v1.1.2 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [56ddb016] ~ Logging ⇒ v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] ~ Pkg ⇒ v1.14.0 [9e88b42a] + Serialization v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [2f01184e] + SparseArrays v1.13.0 [4607b0f0] + SuiteSparse [a4e569a6] + Tar v1.10.0 [8dfed614] ~ Test ⇒ v1.11.0 [deac9b47] + LibCURL_jll v8.18.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.12.2 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.5+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Test Successfully re-resolved Status `/tmp/jl_FZFtDf/Project.toml` [39de3d68] AxisArrays v0.4.8 [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.8.1 [b4f34e82] Distances v0.10.12 [d3d5718d] Diversity v0.5.15 [a58aae7d] EcoBase v0.1.7 [d7ba0133] Git v1.5.0 ⌅ [98e50ef6] JuliaFormatter v1.0.62 [e1d29d7a] Missings v1.2.0 [aea672f4] Phylo v0.5.4 [6f49c342] RCall v0.14.12 [3cdcf5f2] RecipesBase v1.3.4 [58378933] ResearchSoftwareMetadata v0.1.5 [348f2d5d] SpatialEcology v0.9.17 [10745b16] Statistics v1.11.1 [2913bbd2] StatsBase v0.34.10 [b77e0a4c] InteractiveUtils v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [44cfe95a] Pkg v1.14.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_FZFtDf/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [ec485272] ArnoldiMethod v0.4.0 [15f4f7f2] AutoHashEquals v2.2.0 [39de3d68] AxisArrays v0.4.8 [d1d4a3ce] BitFlags v0.1.9 [00ebfdb7] CSTParser v3.4.3 [336ed68f] CSV v0.10.15 [324d7699] CategoricalArrays v1.0.2 [8be319e6] Chain v1.0.0 [944b1d66] CodecZlib v0.7.8 ⌅ [a80b9123] CommonMark v0.8.16 [34da2185] Compat v4.18.1 [f0e56b4a] ConcurrentUtilities v2.5.0 [8f4d0f93] Conda v1.10.3 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [1313f7d8] DataFramesMeta v0.15.6 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [e7dc6d0d] DataValues v0.4.13 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.123 [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 v1.16.0 [d7ba0133] Git v1.5.0 [c27321d9] Glob v1.4.0 ⌃ [86223c79] Graphs v1.13.1 [cd3eb016] HTTP v1.10.19 [34004b35] HypergeometricFunctions v0.3.28 [d25df0c9] Inflate v0.1.5 [842dd82b] InlineStrings v1.4.5 [8197267c] IntervalSets v0.7.13 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [c8e1da08] 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Git_jll v2.53.0+0 [94ce4f54] Libiconv_jll v1.18.0+0 [c8ffd9c3] MbedTLS_jll v2.28.1010+0 [9bd350c2] OpenSSH_jll v10.2.1+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 v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [b27032c2] LibCURL v1.0.0 [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 v1.14.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [1a1011a3] SharedArrays v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [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 v8.18.0+0 [e37daf67] LibGit2_jll v1.9.2+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.30+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.5+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 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... [ 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 ... Matrix data assumed to be presence-absence Matrix data assumed to be presence-absence * 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 ... * 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 Broken Total Time Diversity.jl | 288 2 290 5m30.3s [ Info: Cross validation packages: = Distances = RCall = StatsBase * Validating Distances.jl ... * Validating RCall.jl ... ┌ Warning: RCall.jl: Loading required package: ape │ Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : │ there is no package called ‘ape’ └ @ RCall ~/.julia/packages/RCall/FKyW5/src/io.jl:166 * installing *source* package ‘lattice’ ... ** this is package ‘lattice’ version ‘0.22-9’ ** package ‘lattice’ successfully unpacked and MD5 sums checked ** using staged installation ** libs sh: 1: x86_64-conda-linux-gnu-cc: not found x86_64-conda-linux-gnu-cc -I"/home/pkgeval/.julia/conda/3/x86_64/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/pkgeval/.julia/conda/3/x86_64/include -I/home/pkgeval/.julia/conda/3/x86_64/include -Wl,-rpath-link,/home/pkgeval/.julia/conda/3/x86_64/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/pkgeval/.julia/conda/3/x86_64/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1766426576771/work=/usr/local/src/conda/r-base-4.5.2 -fdebug-prefix-map=/home/pkgeval/.julia/conda/3/x86_64=/usr/local/src/conda-prefix -c init.c -o init.o /bin/sh: 1: x86_64-conda-linux-gnu-cc: not found make: *** [/home/pkgeval/.julia/conda/3/x86_64/lib/R/etc/Makeconf:204: init.o] Error 127 ERROR: compilation failed for package ‘lattice’ * removing ‘/tmp/jl_81GxXd/lattice’ * installing *source* package ‘Rcpp’ ... ** this is package ‘Rcpp’ version ‘1.1.1’ ** package ‘Rcpp’ successfully unpacked and MD5 sums checked ** using staged installation ** libs sh: 1: x86_64-conda-linux-gnu-c++: not found x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/home/pkgeval/.julia/conda/3/x86_64/lib/R/include" -DNDEBUG -I../inst/include/ -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/pkgeval/.julia/conda/3/x86_64/include -I/home/pkgeval/.julia/conda/3/x86_64/include -Wl,-rpath-link,/home/pkgeval/.julia/conda/3/x86_64/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/pkgeval/.julia/conda/3/x86_64/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1766426576771/work=/usr/local/src/conda/r-base-4.5.2 -fdebug-prefix-map=/home/pkgeval/.julia/conda/3/x86_64=/usr/local/src/conda-prefix -c api.cpp -o api.o /bin/sh: 1: x86_64-conda-linux-gnu-c++: not found make: *** [/home/pkgeval/.julia/conda/3/x86_64/lib/R/etc/Makeconf:211: api.o] Error 127 ERROR: compilation failed for package ‘Rcpp’ * removing ‘/tmp/jl_81GxXd/Rcpp’ * installing *source* package ‘digest’ ... ** this is package ‘digest’ version ‘0.6.39’ ** package ‘digest’ successfully unpacked and MD5 sums checked ** using staged installation ** libs sh: 1: x86_64-conda-linux-gnu-cc: not found sh: 1: x86_64-conda-linux-gnu-c++: not found x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/home/pkgeval/.julia/conda/3/x86_64/lib/R/include" -DNDEBUG -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/pkgeval/.julia/conda/3/x86_64/include -I/home/pkgeval/.julia/conda/3/x86_64/include -Wl,-rpath-link,/home/pkgeval/.julia/conda/3/x86_64/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/pkgeval/.julia/conda/3/x86_64/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1766426576771/work=/usr/local/src/conda/r-base-4.5.2 -fdebug-prefix-map=/home/pkgeval/.julia/conda/3/x86_64=/usr/local/src/conda-prefix -c SpookyV2.cpp -o SpookyV2.o /bin/sh: 1: x86_64-conda-linux-gnu-c++: not found make: *** [/home/pkgeval/.julia/conda/3/x86_64/lib/R/etc/Makeconf:211: SpookyV2.o] Error 127 ERROR: compilation failed for package ‘digest’ * removing ‘/tmp/jl_81GxXd/digest’ ERROR: dependency ‘lattice’ is not available for package ‘nlme’ Perhaps try a variation of: install.packages('lattice') * removing ‘/tmp/jl_81GxXd/nlme’ ERROR: dependencies ‘nlme’, ‘lattice’, ‘Rcpp’, ‘digest’ are not available for package ‘ape’ Perhaps try a variation of: install.packages(c('nlme', 'lattice', 'Rcpp', 'digest')) * removing ‘/tmp/jl_81GxXd/ape’ ┌ Warning: RCall.jl: also installing the dependencies ‘nlme’, ‘lattice’, ‘Rcpp’, ‘digest’ │ │ trying URL 'http://cran.r-project.org/src/contrib/nlme_3.1-168.tar.gz' │ trying URL 'http://cran.r-project.org/src/contrib/lattice_0.22-9.tar.gz' │ trying URL 'http://cran.r-project.org/src/contrib/Rcpp_1.1.1.tar.gz' │ trying URL 'http://cran.r-project.org/src/contrib/digest_0.6.39.tar.gz' │ trying URL 'http://cran.r-project.org/src/contrib/ape_5.8-1.tar.gz' │ Warning in install.packages("ape", lib = "/tmp/jl_81GxXd", repos = "http://cran.r-project.org") : │ installation of package ‘lattice’ had non-zero exit status │ Warning in install.packages("ape", lib = "/tmp/jl_81GxXd", repos = "http://cran.r-project.org") : │ installation of package ‘Rcpp’ had non-zero exit status │ Warning in install.packages("ape", lib = "/tmp/jl_81GxXd", repos = "http://cran.r-project.org") : │ installation of package ‘digest’ had non-zero exit status │ Warning in install.packages("ape", lib = "/tmp/jl_81GxXd", repos = "http://cran.r-project.org") : │ installation of package ‘nlme’ had non-zero exit status │ Warning in install.packages("ape", lib = "/tmp/jl_81GxXd", repos = "http://cran.r-project.org") : │ installation of package ‘ape’ had non-zero exit status │ │ The downloaded source packages are in │ ‘/tmp/RtmpVwMSFI/downloaded_packages’ └ @ RCall ~/.julia/packages/RCall/FKyW5/src/io.jl:166 ┌ Warning: RCall.jl: Loading required package: ape │ Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : │ there is no package called ‘ape’ └ @ RCall ~/.julia/packages/RCall/FKyW5/src/io.jl:166 ┌ Warning: ape R package not installed and would not install, skipping R crossvalidation └ @ Main.ValidateRCall.ValidateRCall_rdiversity ~/.julia/packages/Diversity/trAoz/test/run_rcall.jl:28 * Validating StatsBase.jl ... Test Summary: | Pass Total Time test set | 900 900 5m01.8s [ Info: Crosswalk and clean testing: = JuliaFormatter = ResearchSoftwareMetadata * Verifying JuliaFormatter.jl ... fatal: not a git repository (or any parent up to mount point /home/pkgeval/.julia) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). JuliaFormatter: Error During Test at /home/pkgeval/.julia/packages/Diversity/trAoz/test/clean_JuliaFormatter.jl:32 Got exception outside of a @test failed process: Process(setenv(`/home/pkgeval/.julia/artifacts/d43f9e5ac46e24164731f838f2035018de6bfee6/bin/git rev-parse --show-toplevel`,["TAR=tar", "R_RD4PDF=times,inconsolata,hyper", "OPENBLAS_NUM_THREADS=1", "OPENBLAS_MAIN_FREE=1", "JULIA_LOAD_PATH=@:/tmp/jl_FZFtDf", "R_LIBS_SITE=/home/pkgeval/.julia/conda/3/x86_64/lib/R/site-library", "JULIA_DEPOT_PATH=/home/pkgeval/.julia:/usr/local/share/julia:", "LN_S=ln -s", "R_ZIPCMD=", "R_UNZIPCMD=", "R_SHARE_DIR=/home/pkgeval/.julia/conda/3/x86_64/lib/R/share", "PYTHON=", "R_LIBS_USER=/home/pkgeval/R/x86_64-conda-linux-gnu-library/4.5", "R_STRIP_SHARED_LIB=x86_64-conda-linux-gnu-strip --strip-unneeded", "LD_LIBRARY_PATH=/opt/julia/bin/../lib/julia:/home/pkgeval/.julia/artifacts/0ea6a498a51da4141980859d84bdf5a897e03fda/lib:/home/pkgeval/.julia/artifacts/5acd766faaca59c3c1f3cfa67e2bf6dcf1e3e883/lib", "R_BZIPCMD=/home/conda/feedstock_root/build_artifacts/r-base-split_1766426576771/_build_env/bin/bzip2", "DISPLAY=:1", "PKGEVAL=true", "LANG=C.UTF-8", "R_PLATFORM=x86_64-conda-linux-gnu", "R_STRIP_STATIC_LIB=x86_64-conda-linux-gnu-strip --strip-debug", "R_GZIPCMD=gzip", "JULIA_PKG_PRECOMPILE_AUTO=0", "JULIA_PKGEVAL=true", "PATH=/home/pkgeval/.julia/artifacts/65b962c68bed01a34a1a9ee23cbdde4dc3fe2246/bin:/home/pkgeval/.julia/artifacts/d43f9e5ac46e24164731f838f2035018de6bfee6/bin:/home/pkgeval/.julia/artifacts/fc7cfafb3218745ad80066127ae3decb2c8a31f6/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/opt/julia/bin", "EDITOR=vi", "GIT_SSL_CAINFO=/opt/julia/share/julia/cert.pem", "GIT_TEMPLATE_DIR=/home/pkgeval/.julia/artifacts/d43f9e5ac46e24164731f838f2035018de6bfee6/share/git-core/templates", "R_PAPERSIZE=a4", "CI=true", "JULIA_CPU_THREADS=1", "R_PRINTCMD=", "R_HOME=/home/pkgeval/.julia/conda/3/x86_64/lib/R", "PAGER=less", "JULIA_NUM_PRECOMPILE_TASKS=1", "GIT_EXEC_PATH=/home/pkgeval/.julia/artifacts/d43f9e5ac46e24164731f838f2035018de6bfee6/libexec/git-core", "R_BROWSER=", "MAKE=make", "R_SESSION_TMPDIR=/tmp/RtmpVwMSFI", "R_TEXI2DVICMD=/home/conda/feedstock_root/build_artifacts/r-base-split_1766426576771/_build_env/bin/texi2dvi", "SED=/home/pkgeval/.julia/conda/3/x86_64/bin/sed", "HOME=/home/pkgeval", "JULIA_NUM_THREADS=1", "R_PDFVIEWER=", "R_INCLUDE_DIR=/home/pkgeval/.julia/conda/3/x86_64/lib/R/include", "R_DOC_DIR=/home/pkgeval/.julia/conda/3/x86_64/lib/R/doc"]), ProcessExited(128)) [128] Stacktrace: [1] pipeline_error @ ./process.jl:610 [inlined] [2] read(cmd::Cmd) @ Base ./process.jl:490 [3] read @ ./process.jl:499 [inlined] [4] readchomp(x::Cmd) @ Base ./io.jl:1154 [5] top-level scope @ ~/.julia/packages/Diversity/trAoz/test/clean_JuliaFormatter.jl:33 [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2244 [inlined] [7] macro expansion @ ~/.julia/packages/Diversity/trAoz/test/clean_JuliaFormatter.jl:33 [inlined] [8] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [9] top-level scope @ ~/.julia/packages/Diversity/trAoz/test/runtests.jl:150 [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2244 [inlined] [11] macro expansion @ ~/.julia/packages/Diversity/trAoz/test/runtests.jl:155 [inlined] [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2325 [inlined] [13] macro expansion @ ~/.julia/packages/Diversity/trAoz/test/runtests.jl:158 [inlined] [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [15] top-level scope @ none:6 [16] eval(m::Module, e::Any) @ Core ./boot.jl:489 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [18] _start() @ Base ./client.jl:585 * Verifying ResearchSoftwareMetadata.jl ... fatal: not a git repository (or any parent up to mount point /home/pkgeval/.julia) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). RSMD: Error During Test at /home/pkgeval/.julia/packages/Diversity/trAoz/test/clean_ResearchSoftwareMetadata.jl:32 Got exception outside of a @test failed process: Process(setenv(`/home/pkgeval/.julia/artifacts/d43f9e5ac46e24164731f838f2035018de6bfee6/bin/git rev-parse --show-toplevel`,["TAR=tar", "R_RD4PDF=times,inconsolata,hyper", "OPENBLAS_NUM_THREADS=1", "OPENBLAS_MAIN_FREE=1", "JULIA_LOAD_PATH=@:/tmp/jl_FZFtDf", "R_LIBS_SITE=/home/pkgeval/.julia/conda/3/x86_64/lib/R/site-library", "JULIA_DEPOT_PATH=/home/pkgeval/.julia:/usr/local/share/julia:", "LN_S=ln -s", "R_ZIPCMD=", "R_UNZIPCMD=", "R_SHARE_DIR=/home/pkgeval/.julia/conda/3/x86_64/lib/R/share", "PYTHON=", "R_LIBS_USER=/home/pkgeval/R/x86_64-conda-linux-gnu-library/4.5", "R_STRIP_SHARED_LIB=x86_64-conda-linux-gnu-strip --strip-unneeded", "LD_LIBRARY_PATH=/opt/julia/bin/../lib/julia:/home/pkgeval/.julia/artifacts/0ea6a498a51da4141980859d84bdf5a897e03fda/lib:/home/pkgeval/.julia/artifacts/5acd766faaca59c3c1f3cfa67e2bf6dcf1e3e883/lib", "R_BZIPCMD=/home/conda/feedstock_root/build_artifacts/r-base-split_1766426576771/_build_env/bin/bzip2", "DISPLAY=:1", "PKGEVAL=true", "LANG=C.UTF-8", "R_PLATFORM=x86_64-conda-linux-gnu", "R_STRIP_STATIC_LIB=x86_64-conda-linux-gnu-strip --strip-debug", "R_GZIPCMD=gzip", "JULIA_PKG_PRECOMPILE_AUTO=0", "JULIA_PKGEVAL=true", "PATH=/home/pkgeval/.julia/artifacts/65b962c68bed01a34a1a9ee23cbdde4dc3fe2246/bin:/home/pkgeval/.julia/artifacts/d43f9e5ac46e24164731f838f2035018de6bfee6/bin:/home/pkgeval/.julia/artifacts/fc7cfafb3218745ad80066127ae3decb2c8a31f6/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/opt/julia/bin", "EDITOR=vi", "GIT_SSL_CAINFO=/opt/julia/share/julia/cert.pem", "GIT_TEMPLATE_DIR=/home/pkgeval/.julia/artifacts/d43f9e5ac46e24164731f838f2035018de6bfee6/share/git-core/templates", "R_PAPERSIZE=a4", "CI=true", "JULIA_CPU_THREADS=1", "R_PRINTCMD=", "R_HOME=/home/pkgeval/.julia/conda/3/x86_64/lib/R", "PAGER=less", "JULIA_NUM_PRECOMPILE_TASKS=1", "GIT_EXEC_PATH=/home/pkgeval/.julia/artifacts/d43f9e5ac46e24164731f838f2035018de6bfee6/libexec/git-core", "R_BROWSER=", "MAKE=make", "R_SESSION_TMPDIR=/tmp/RtmpVwMSFI", "R_TEXI2DVICMD=/home/conda/feedstock_root/build_artifacts/r-base-split_1766426576771/_build_env/bin/texi2dvi", "SED=/home/pkgeval/.julia/conda/3/x86_64/bin/sed", "HOME=/home/pkgeval", "JULIA_NUM_THREADS=1", "R_PDFVIEWER=", "R_INCLUDE_DIR=/home/pkgeval/.julia/conda/3/x86_64/lib/R/include", "R_DOC_DIR=/home/pkgeval/.julia/conda/3/x86_64/lib/R/doc"]), ProcessExited(128)) [128] Stacktrace: [1] pipeline_error @ ./process.jl:610 [inlined] [2] read(cmd::Cmd) @ Base ./process.jl:490 [3] read @ ./process.jl:499 [inlined] [4] readchomp(x::Cmd) @ Base ./io.jl:1154 [5] top-level scope @ ~/.julia/packages/Diversity/trAoz/test/clean_ResearchSoftwareMetadata.jl:33 [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2244 [inlined] [7] macro expansion @ ~/.julia/packages/Diversity/trAoz/test/clean_ResearchSoftwareMetadata.jl:33 [inlined] [8] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [9] top-level scope @ ~/.julia/packages/Diversity/trAoz/test/runtests.jl:150 [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2244 [inlined] [11] macro expansion @ ~/.julia/packages/Diversity/trAoz/test/runtests.jl:155 [inlined] [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2325 [inlined] [13] macro expansion @ ~/.julia/packages/Diversity/trAoz/test/runtests.jl:158 [inlined] [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [15] top-level scope @ none:6 [16] eval(m::Module, e::Any) @ Core ./boot.jl:489 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [18] _start() @ Base ./client.jl:585 Test Summary: | Error Total Time test set | 2 2 14.7s c = JuliaFormatter | 1 1 11.8s JuliaFormatter | 1 1 9.1s c = ResearchSoftwareMetadata | 1 1 2.9s RSMD | 1 1 0.0s RNG of the outermost testset: Xoshiro(0x9951797c85a704f1, 0xb9d66be14dfba82b, 0xb170153285fd9556, 0xe90a07f7bdd1fd77, 0x9d4b5ee33e4bd661) ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 2 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/Diversity/trAoz/test/runtests.jl:139 Testing failed after 674.25s ERROR: LoadError: Package Diversity errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/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/v1.14/Pkg/src/Operations.jl:3138 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3003 [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/v1.14/Pkg/src/API.jl:586 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:562 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1139.78s: package tests unexpectedly errored