Package evaluation of Diversity on Julia 1.11.5 (32ac370b68*) started at 2025-06-29T09:39:04.349 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.03s ################################################################################ # Installation # Installing Diversity... Resolving package versions... Installed DataAPI ───────────────────── v1.16.0 Installed PooledArrays ──────────────── v1.4.3 Installed Tables ────────────────────── v1.12.1 Installed TableTraits ───────────────── v1.0.1 Installed Preferences ───────────────── v1.4.3 Installed SentinelArrays ────────────── v1.4.8 Installed Crayons ───────────────────── v4.1.1 Installed RecipesBase ───────────────── v1.3.4 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed InlineStrings ─────────────── v1.4.4 Installed DataValueInterfaces ───────── v1.0.0 Installed PrettyTables ──────────────── v2.4.0 Installed PrecompileTools ───────────── v1.2.1 Installed OrderedCollections ────────── v1.8.1 Installed InvertedIndices ───────────── v1.3.1 Installed Reexport ──────────────────── v1.2.2 Installed Statistics ────────────────── v1.11.1 Installed DataStructures ────────────── v0.18.22 Installed LaTeXStrings ──────────────── v1.4.0 Installed Diversity ─────────────────── v0.5.15 Installed DataFrames ────────────────── v1.7.0 Installed Compat ────────────────────── v4.16.0 Installed StringManipulation ────────── v0.4.1 Installed Missings ──────────────────── v1.2.0 Installed SortingAlgorithms ─────────── v1.2.1 Installed EcoBase ───────────────────── v0.1.7 Updating `~/.julia/environments/v1.11/Project.toml` [d3d5718d] + Diversity v0.5.15 Updating `~/.julia/environments/v1.11/Manifest.toml` [34da2185] + Compat v4.16.0 [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 v1.2.1 [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 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [d6f4376e] + Markdown v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [4536629a] + OpenBLAS_jll v0.3.27+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 3.68s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 2419.5 ms ✓ TestEnv 1 dependency successfully precompiled in 3 seconds. 23 already precompiled. Precompiling package dependencies... Precompilation completed after 844.84s ################################################################################ # Testing # Testing Diversity Status `/tmp/jl_BB8CLk/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 v1.11.0 [56ddb016] Logging v1.11.0 [44cfe95a] Pkg v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_BB8CLk/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 v4.16.0 [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 v1.2.1 [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 [9bd350c2] OpenSSH_jll v10.0.1+0 [458c3c95] OpenSSL_jll v3.5.0+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 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.11.0 [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 v1.11.0 [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 v1.1.1+0 [deac9b47] LibCURL_jll v8.6.0+0 [e37daf67] LibGit2_jll v1.7.2+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.6+0 [14a3606d] MozillaCACerts_jll v2023.12.12 [4536629a] OpenBLAS_jll v0.3.27+1 [05823500] OpenLibm_jll v0.8.5+0 [efcefdf7] PCRE2_jll v10.42.0+1 [bea87d4a] SuiteSparse_jll v7.7.0+0 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.59.0+0 [3f19e933] p7zip_jll v17.4.0+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 SpatialEcology... 1918.4 ms ✓ RandomBooleanMatrices 4760.1 ms ✓ DataFramesMeta Info Given SpatialEcology was explicitly requested, output will be shown live  WARNING: could not import DataFrames.aggregate into SpatialEcology 5766.8 ms ✓ SpatialEcology 3 dependencies successfully precompiled in 13 seconds. 51 already precompiled. 1 dependency had output during precompilation: ┌ SpatialEcology │ [Output was shown above] └ 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 ... Precompiling DiversityAxisArraysExt... 3803.4 ms ✓ Diversity → DiversityAxisArraysExt 1 dependency successfully precompiled in 4 seconds. 43 already precompiled. Precompiling DistributionsTestExt... 2727.6 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 3 seconds. 48 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 Broken Total Time Diversity.jl | 288 2 290 7m44.5s [ 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/WTNSB/src/io.jl:171 * installing *source* package ‘lattice’ ... ** 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_1747311753578/work=/usr/local/src/conda/r-base-4.4.3 -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:197: init.o] Error 127 ERROR: compilation failed for package ‘lattice’ * removing ‘/tmp/jl_NpBQbN/lattice’ * installing *source* package ‘Rcpp’ ... ** 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_1747311753578/work=/usr/local/src/conda/r-base-4.4.3 -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:204: api.o] Error 127 ERROR: compilation failed for package ‘Rcpp’ * removing ‘/tmp/jl_NpBQbN/Rcpp’ * installing *source* package ‘digest’ ... ** 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_1747311753578/work=/usr/local/src/conda/r-base-4.4.3 -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:204: SpookyV2.o] Error 127 ERROR: compilation failed for package ‘digest’ * removing ‘/tmp/jl_NpBQbN/digest’ ERROR: dependency ‘lattice’ is not available for package ‘nlme’ * removing ‘/tmp/jl_NpBQbN/nlme’ ERROR: dependencies ‘nlme’, ‘lattice’, ‘Rcpp’, ‘digest’ are not available for package ‘ape’ * removing ‘/tmp/jl_NpBQbN/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' │ Content type 'application/x-gzip' length 860576 bytes (840 KB) │ ================================================== │ downloaded 840 KB │ │ trying URL 'http://cran.r-project.org/src/contrib/lattice_0.22-7.tar.gz' │ Content type 'application/x-gzip' length 598622 bytes (584 KB) │ ================================================== │ downloaded 584 KB │ │ trying URL 'http://cran.r-project.org/src/contrib/Rcpp_1.0.14.tar.gz' │ Content type 'application/x-gzip' length 3013288 bytes (2.9 MB) │ ================================================== │ downloaded 2.9 MB │ │ trying URL 'http://cran.r-project.org/src/contrib/digest_0.6.37.tar.gz' │ Content type 'application/x-gzip' length 232306 bytes (226 KB) │ ================================================== │ downloaded 226 KB │ │ trying URL 'http://cran.r-project.org/src/contrib/ape_5.8-1.tar.gz' │ Content type 'application/x-gzip' length 1424541 bytes (1.4 MB) │ ================================================== │ downloaded 1.4 MB │ │ Warning in install.packages("ape", lib = "/tmp/jl_NpBQbN", repos = "http://cran.r-project.org") : │ installation of package ‘lattice’ had non-zero exit status │ Warning in install.packages("ape", lib = "/tmp/jl_NpBQbN", repos = "http://cran.r-project.org") : │ installation of package ‘Rcpp’ had non-zero exit status │ Warning in install.packages("ape", lib = "/tmp/jl_NpBQbN", repos = "http://cran.r-project.org") : │ installation of package ‘digest’ had non-zero exit status │ Warning in install.packages("ape", lib = "/tmp/jl_NpBQbN", repos = "http://cran.r-project.org") : │ installation of package ‘nlme’ had non-zero exit status │ Warning in install.packages("ape", lib = "/tmp/jl_NpBQbN", repos = "http://cran.r-project.org") : │ installation of package ‘ape’ had non-zero exit status │ │ The downloaded source packages are in │ ‘/tmp/RtmpcNxjxL/downloaded_packages’ └ @ RCall ~/.julia/packages/RCall/WTNSB/src/io.jl:171 ┌ 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/WTNSB/src/io.jl:171 ┌ 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 4m47.7s [ Info: Crosswalk and clean testing: = JuliaFormatter = ResearchSoftwareMetadata * Verifying JuliaFormatter.jl ... fatal: not a git repository (or any parent up to mount point /home) 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/b48e71be9a4d84229c2a0ff6bd382c2654c08396/bin/git rev-parse --show-toplevel`,["PATH=/home/pkgeval/.julia/artifacts/b48e71be9a4d84229c2a0ff6bd382c2654c08396/bin:/home/pkgeval/.julia/artifacts/7b46720b034a5501393d9cbb503824d984b6c3d0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin", "EDITOR=vi", "R_LIBS_USER=/home/pkgeval/R/x86_64-conda-linux-gnu-library/4.4", "R_PDFVIEWER=", "LD_LIBRARY_PATH=/opt/julia/bin/../lib/julia:/home/pkgeval/.julia/artifacts/96bc7b9ddb319d1a051535c85184aa2bf42dbd8b/lib:/home/pkgeval/.julia/artifacts/a696e1e3e6b8d3c2c4b67609357ebc5c35eabde1/lib:/home/pkgeval/.julia/artifacts/5acd766faaca59c3c1f3cfa67e2bf6dcf1e3e883/lib", "R_INCLUDE_DIR=/home/pkgeval/.julia/conda/3/x86_64/lib/R/include", "R_TEXI2DVICMD=/home/conda/feedstock_root/build_artifacts/r-base-split_1747311753578/_build_env/bin/texi2dvi", "R_HOME=/home/pkgeval/.julia/conda/3/x86_64/lib/R", "R_BZIPCMD=/home/conda/feedstock_root/build_artifacts/r-base-split_1747311753578/_build_env/bin/bzip2", "SED=/home/pkgeval/.julia/conda/3/x86_64/bin/sed", "GIT_TEMPLATE_DIR=/home/pkgeval/.julia/artifacts/b48e71be9a4d84229c2a0ff6bd382c2654c08396/share/git-core/templates", "PKGEVAL=true", "JULIA_DEPOT_PATH=/home/pkgeval/.julia:/usr/local/share/julia:", "TAR=tar", "R_PLATFORM=x86_64-conda-linux-gnu", "R_STRIP_SHARED_LIB=x86_64-conda-linux-gnu-strip --strip-unneeded", "R_STRIP_STATIC_LIB=x86_64-conda-linux-gnu-strip --strip-debug", "HOME=/home/pkgeval", "JULIA_PKGEVAL=true", "PYTHON=", "R_GZIPCMD=gzip", "GIT_EXEC_PATH=/home/pkgeval/.julia/artifacts/b48e71be9a4d84229c2a0ff6bd382c2654c08396/libexec/git-core", "MAKE=make", "R_SESSION_TMPDIR=/tmp/RtmpcNxjxL", "R_PAPERSIZE=a4", "LANG=C.UTF-8", "JULIA_CPU_THREADS=1", "PAGER=less", "R_RD4PDF=times,inconsolata,hyper", "JULIA_PKG_PRECOMPILE_AUTO=0", "JULIA_NUM_THREADS=1", "R_LIBS_SITE=/home/pkgeval/.julia/conda/3/x86_64/lib/R/site-library", "DISPLAY=:1", "R_ZIPCMD=", "OPENBLAS_NUM_THREADS=1", "CI=true", "JULIA_NUM_PRECOMPILE_TASKS=1", "R_UNZIPCMD=", "R_BROWSER=", "JULIA_LOAD_PATH=@:/tmp/jl_BB8CLk", "R_PRINTCMD=", "R_SHARE_DIR=/home/pkgeval/.julia/conda/3/x86_64/lib/R/share", "GIT_SSL_CAINFO=/opt/julia/share/julia/cert.pem", "R_DOC_DIR=/home/pkgeval/.julia/conda/3/x86_64/lib/R/doc", "OPENBLAS_MAIN_FREE=1", "LN_S=ln -s"]), ProcessExited(128)) [128] Stacktrace: [1] pipeline_error @ ./process.jl:598 [inlined] [2] read(cmd::Cmd) @ Base ./process.jl:482 [3] read @ ./process.jl:491 [inlined] [4] readchomp(x::Cmd) @ Base ./io.jl:1136 [5] macro expansion @ ~/.julia/packages/Diversity/trAoz/test/clean_JuliaFormatter.jl:33 [inlined] [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [7] top-level scope @ ~/.julia/packages/Diversity/trAoz/test/clean_JuliaFormatter.jl:33 [8] include(fname::String) @ Main ./sysimg.jl:38 [9] macro expansion @ ~/.julia/packages/Diversity/trAoz/test/runtests.jl:158 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1798 [inlined] [11] macro expansion @ ~/.julia/packages/Diversity/trAoz/test/runtests.jl:155 [inlined] [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [13] top-level scope @ ~/.julia/packages/Diversity/trAoz/test/runtests.jl:150 [14] include(fname::String) @ Main ./sysimg.jl:38 [15] top-level scope @ none:6 * Verifying ResearchSoftwareMetadata.jl ... fatal: not a git repository (or any parent up to mount point /home) 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/b48e71be9a4d84229c2a0ff6bd382c2654c08396/bin/git rev-parse --show-toplevel`,["PATH=/home/pkgeval/.julia/artifacts/b48e71be9a4d84229c2a0ff6bd382c2654c08396/bin:/home/pkgeval/.julia/artifacts/7b46720b034a5501393d9cbb503824d984b6c3d0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin", "EDITOR=vi", "R_LIBS_USER=/home/pkgeval/R/x86_64-conda-linux-gnu-library/4.4", "R_PDFVIEWER=", "LD_LIBRARY_PATH=/opt/julia/bin/../lib/julia:/home/pkgeval/.julia/artifacts/96bc7b9ddb319d1a051535c85184aa2bf42dbd8b/lib:/home/pkgeval/.julia/artifacts/a696e1e3e6b8d3c2c4b67609357ebc5c35eabde1/lib:/home/pkgeval/.julia/artifacts/5acd766faaca59c3c1f3cfa67e2bf6dcf1e3e883/lib", "R_INCLUDE_DIR=/home/pkgeval/.julia/conda/3/x86_64/lib/R/include", "R_TEXI2DVICMD=/home/conda/feedstock_root/build_artifacts/r-base-split_1747311753578/_build_env/bin/texi2dvi", "R_HOME=/home/pkgeval/.julia/conda/3/x86_64/lib/R", "R_BZIPCMD=/home/conda/feedstock_root/build_artifacts/r-base-split_1747311753578/_build_env/bin/bzip2", "SED=/home/pkgeval/.julia/conda/3/x86_64/bin/sed", "GIT_TEMPLATE_DIR=/home/pkgeval/.julia/artifacts/b48e71be9a4d84229c2a0ff6bd382c2654c08396/share/git-core/templates", "PKGEVAL=true", "JULIA_DEPOT_PATH=/home/pkgeval/.julia:/usr/local/share/julia:", "TAR=tar", "R_PLATFORM=x86_64-conda-linux-gnu", "R_STRIP_SHARED_LIB=x86_64-conda-linux-gnu-strip --strip-unneeded", "R_STRIP_STATIC_LIB=x86_64-conda-linux-gnu-strip --strip-debug", "HOME=/home/pkgeval", "JULIA_PKGEVAL=true", "PYTHON=", "R_GZIPCMD=gzip", "GIT_EXEC_PATH=/home/pkgeval/.julia/artifacts/b48e71be9a4d84229c2a0ff6bd382c2654c08396/libexec/git-core", "MAKE=make", "R_SESSION_TMPDIR=/tmp/RtmpcNxjxL", "R_PAPERSIZE=a4", "LANG=C.UTF-8", "JULIA_CPU_THREADS=1", "PAGER=less", "R_RD4PDF=times,inconsolata,hyper", "JULIA_PKG_PRECOMPILE_AUTO=0", "JULIA_NUM_THREADS=1", "R_LIBS_SITE=/home/pkgeval/.julia/conda/3/x86_64/lib/R/site-library", "DISPLAY=:1", "R_ZIPCMD=", "OPENBLAS_NUM_THREADS=1", "CI=true", "JULIA_NUM_PRECOMPILE_TASKS=1", "R_UNZIPCMD=", "R_BROWSER=", "JULIA_LOAD_PATH=@:/tmp/jl_BB8CLk", "R_PRINTCMD=", "R_SHARE_DIR=/home/pkgeval/.julia/conda/3/x86_64/lib/R/share", "GIT_SSL_CAINFO=/opt/julia/share/julia/cert.pem", "R_DOC_DIR=/home/pkgeval/.julia/conda/3/x86_64/lib/R/doc", "OPENBLAS_MAIN_FREE=1", "LN_S=ln -s"]), ProcessExited(128)) [128] Stacktrace: [1] pipeline_error @ ./process.jl:598 [inlined] [2] read(cmd::Cmd) @ Base ./process.jl:482 [3] read @ ./process.jl:491 [inlined] [4] readchomp(x::Cmd) @ Base ./io.jl:1136 [5] macro expansion @ ~/.julia/packages/Diversity/trAoz/test/clean_ResearchSoftwareMetadata.jl:33 [inlined] [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [7] top-level scope @ ~/.julia/packages/Diversity/trAoz/test/clean_ResearchSoftwareMetadata.jl:33 [8] include(fname::String) @ Main ./sysimg.jl:38 [9] macro expansion @ ~/.julia/packages/Diversity/trAoz/test/runtests.jl:158 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1798 [inlined] [11] macro expansion @ ~/.julia/packages/Diversity/trAoz/test/runtests.jl:155 [inlined] [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [13] top-level scope @ ~/.julia/packages/Diversity/trAoz/test/runtests.jl:150 [14] include(fname::String) @ Main ./sysimg.jl:38 [15] top-level scope @ none:6 Test Summary: | Error Total Time test set | 2 2 15.8s c = JuliaFormatter | 1 1 12.8s JuliaFormatter | 1 1 9.7s c = ResearchSoftwareMetadata | 1 1 3.0s RSMD | 1 1 0.2s 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 779.49s ERROR: LoadError: Package Diversity errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.11/Pkg/src/Operations.jl:2128 [3] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2011 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.11/Pkg/src/API.jl:481 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1710.17s: package tests unexpectedly errored