Package evaluation of Diversity on Julia 1.12.0-DEV.1805 (a080deafdd*) started at 2025-03-24T14:46:16.999 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.99s ################################################################################ # 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 v4.16.0 [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 v1.4.3 [41ab1584] + InvertedIndices v1.3.1 [82899510] + IteratorInterfaceExtensions v1.0.0 [b964fa9f] + LaTeXStrings v1.4.0 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.0 [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 v1.12.0 [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 [dc6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [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 [f489334b] + StyledStrings v1.11.0 [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.2.0+0 [4536629a] + OpenBLAS_jll v0.3.28+3 [8e850b90] + libblastrampoline_jll v5.11.2+0 Installation completed after 3.63s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 583.76s ################################################################################ # Testing # Testing Diversity Status `/tmp/jl_SIxBsW/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 v1.3.1 [98e50ef6] JuliaFormatter v1.0.62 [e1d29d7a] Missings v1.2.0 [aea672f4] Phylo v0.5.4 [6f49c342] RCall v0.14.6 [3cdcf5f2] RecipesBase v1.3.4 [58378933] ResearchSoftwareMetadata v0.1.4 [348f2d5d] SpatialEcology v0.9.16 [10745b16] Statistics v1.11.1 [2913bbd2] StatsBase v0.34.4 [b77e0a4c] InteractiveUtils v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [44cfe95a] Pkg v1.12.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_SIxBsW/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 v0.8.15 [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 v0.25.118 [d3d5718d] Diversity v0.5.15 [ffbed154] DocStringExtensions v0.9.3 [a58aae7d] EcoBase v0.1.7 [460bff9d] ExceptionUnwrapping v0.1.11 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.13.0 [d7ba0133] Git v1.3.1 [c27321d9] Glob v1.3.1 [86223c79] Graphs v1.12.0 [cd3eb016] HTTP v1.10.15 [34004b35] HypergeometricFunctions v0.3.28 [d25df0c9] Inflate v0.1.5 [842dd82b] InlineStrings v1.4.3 [8197267c] IntervalSets v0.7.10 [41ab1584] 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[a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.2.0+0 [deac9b47] LibCURL_jll v8.6.0+0 [e37daf67] LibGit2_jll v1.8.0+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.6+1 [14a3606d] MozillaCACerts_jll v2024.11.26 [4536629a] OpenBLAS_jll v0.3.28+3 [05823500] OpenLibm_jll v0.8.1+3 [efcefdf7] PCRE2_jll v10.44.0+0 [bea87d4a] SuiteSparse_jll v7.8.0+1 [83775a58] Zlib_jll v1.3.1+1 [8e850b90] libblastrampoline_jll v5.11.2+0 [8e850ede] nghttp2_jll v1.63.0+1 [3f19e933] p7zip_jll v17.5.0+1 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 ... WARNING: could not import DataFrames.aggregate into SpatialEcology 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 7m35.8s [ 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/0ggIQ/src/io.jl:172 * 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=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -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:193: init.o] Error 127 ERROR: compilation failed for package ‘lattice’ * removing ‘/tmp/jl_jktDFo/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=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -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:200: api.o] Error 127 ERROR: compilation failed for package ‘Rcpp’ * removing ‘/tmp/jl_jktDFo/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=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -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:200: SpookyV2.o] Error 127 ERROR: compilation failed for package ‘digest’ * removing ‘/tmp/jl_jktDFo/digest’ ERROR: dependency ‘lattice’ is not available for package ‘nlme’ * removing ‘/tmp/jl_jktDFo/nlme’ ERROR: dependencies ‘nlme’, ‘lattice’, ‘Rcpp’, ‘digest’ are not available for package ‘ape’ * removing ‘/tmp/jl_jktDFo/ape’ ┌ Warning: RCall.jl: also installing the dependencies ‘nlme’, ‘lattice’, ‘Rcpp’, ‘digest’ │ │ trying URL 'http://cran.r-project.org/src/contrib/nlme_3.1-167.tar.gz' │ Content type 'application/x-gzip' length 849418 bytes (829 KB) │ ================================================== │ downloaded 829 KB │ │ trying URL 'http://cran.r-project.org/src/contrib/lattice_0.22-6.tar.gz' │ Content type 'application/x-gzip' length 598581 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_jktDFo", repos = "http://cran.r-project.org") : │ installation of package ‘lattice’ had non-zero exit status │ Warning in install.packages("ape", lib = "/tmp/jl_jktDFo", repos = "http://cran.r-project.org") : │ installation of package ‘Rcpp’ had non-zero exit status │ Warning in install.packages("ape", lib = "/tmp/jl_jktDFo", repos = "http://cran.r-project.org") : │ installation of package ‘digest’ had non-zero exit status │ Warning in install.packages("ape", lib = "/tmp/jl_jktDFo", repos = "http://cran.r-project.org") : │ installation of package ‘nlme’ had non-zero exit status │ Warning in install.packages("ape", lib = "/tmp/jl_jktDFo", repos = "http://cran.r-project.org") : │ installation of package ‘ape’ had non-zero exit status │ │ The downloaded source packages are in │ ‘/tmp/RtmpvigUw6/downloaded_packages’ └ @ RCall ~/.julia/packages/RCall/0ggIQ/src/io.jl:172 ┌ 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/0ggIQ/src/io.jl:172 ┌ 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 7m31.1s [ 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/8a0f840ec3a4b7913b278fad357755c65b097456/bin/git rev-parse --show-toplevel`,["PATH=/home/pkgeval/.julia/artifacts/96bc7b9ddb319d1a051535c85184aa2bf42dbd8b/bin:/home/pkgeval/.julia/artifacts/8be4b2d49ed77db4f9607e5f8a7b09cc105be2ee/bin:/home/pkgeval/.julia/artifacts/8a0f840ec3a4b7913b278fad357755c65b097456/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/4.3", "R_PDFVIEWER=", "LD_LIBRARY_PATH=/opt/julia/bin/../lib/julia:/home/pkgeval/.julia/artifacts/96bc7b9ddb319d1a051535c85184aa2bf42dbd8b/lib:/home/pkgeval/.julia/artifacts/8be4b2d49ed77db4f9607e5f8a7b09cc105be2ee/lib:/home/pkgeval/.julia/artifacts/5acd766faaca59c3c1f3cfa67e2bf6dcf1e3e883/lib:/opt/julia/bin/../lib/julia:/opt/julia/bin/../lib", "R_INCLUDE_DIR=/home/pkgeval/.julia/conda/3/x86_64/lib/R/include", "R_TEXI2DVICMD=/workspace/croot/r-base_1695428141831/_build_env/bin/texi2dvi", "R_HOME=/home/pkgeval/.julia/conda/3/x86_64/lib/R", "R_BZIPCMD=/home/pkgeval/.julia/conda/3/x86_64/bin/bzip2", "SED=/usr/bin/sed", "GIT_TEMPLATE_DIR=/home/pkgeval/.julia/artifacts/8a0f840ec3a4b7913b278fad357755c65b097456/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", "HOME=/home/pkgeval", "R_STRIP_STATIC_LIB=x86_64-conda-linux-gnu-strip --strip-debug", "JULIA_PKGEVAL=true", "PYTHON=", "R_GZIPCMD=gzip", "GIT_EXEC_PATH=/home/pkgeval/.julia/artifacts/8a0f840ec3a4b7913b278fad357755c65b097456/libexec/git-core", "MAKE=make", "R_SESSION_TMPDIR=/tmp/RtmpvigUw6", "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_SYSTEM_ABI=linux,gcc,gxx,gfortran,gfortran", "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_SIxBsW", "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:1137 [5] top-level scope @ ~/.julia/packages/Diversity/trAoz/test/clean_JuliaFormatter.jl:33 [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1724 [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:301 [9] top-level scope @ ~/.julia/packages/Diversity/trAoz/test/runtests.jl:150 [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1724 [inlined] [11] macro expansion @ ~/.julia/packages/Diversity/trAoz/test/runtests.jl:155 [inlined] [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1813 [inlined] [13] macro expansion @ ~/.julia/packages/Diversity/trAoz/test/runtests.jl:158 [inlined] [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:301 [15] top-level scope @ none:6 [16] eval(m::Module, e::Any) @ Core ./boot.jl:485 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:295 [18] _start() @ Base ./client.jl:558 * Verifying ResearchSoftwareMetadata.jl ... ┌ Info: Ignoring an error that occurred during the precompilation workload │ exception = │ HTTP.ConnectError for url = `https://localhost:57813`: IOError: connect: connection refused (ECONNREFUSED) │ Stacktrace: │ [1] getconnection(::Type{Sockets.TCPSocket}, host::SubString{String}, port::SubString{String}; keepalive::Bool, readtimeout::Int64, kw::@Kwargs{require_ssl_verification::Bool, iofunction::Nothing, decompress::Nothing, verbose::Int64}) │ @ HTTP.Connections ~/.julia/packages/HTTP/4AUPl/src/Connections.jl:531 │ [2] getconnection │ @ ~/.julia/packages/HTTP/4AUPl/src/Connections.jl:508 [inlined] │ [3] getconnection(::Type{OpenSSL.SSLStream}, host::SubString{String}, port::SubString{String}; kw::@Kwargs{require_ssl_verification::Bool, keepalive::Bool, readtimeout::Int64, iofunction::Nothing, decompress::Nothing, verbose::Int64}) │ @ HTTP.Connections ~/.julia/packages/HTTP/4AUPl/src/Connections.jl:585 │ [4] getconnection │ @ ~/.julia/packages/HTTP/4AUPl/src/Connections.jl:578 [inlined] │ [5] #13 │ @ ~/.julia/packages/HTTP/4AUPl/src/Connections.jl:467 [inlined] │ [6] macro expansion │ @ ~/.julia/packages/ConcurrentUtilities/ofY4K/src/try_with_timeout.jl:92 [inlined] │ [7] (::ConcurrentUtilities.var"#try_with_timeout##2#try_with_timeout##3"{Any, Channel{Any}, HTTP.Connections.var"#13#14"{OpenSSL.SSLStream, Bool, Bool, @Kwargs{readtimeout::Int64, iofunction::Nothing, decompress::Nothing, verbose::Int64}, SubString{String}, SubString{String}}, Timer})() │ @ ConcurrentUtilities ~/.julia/packages/ConcurrentUtilities/ofY4K/src/ConcurrentUtilities.jl:10 │ Stacktrace: │ [1] (::HTTP.ConnectionRequest.var"#connections#connectionlayer##0"{HTTP.ConnectionRequest.var"#connections#1#connectionlayer##1"{HTTP.TimeoutRequest.var"#timeouts#timeoutlayer##0"{HTTP.TimeoutRequest.var"#timeouts#1#timeoutlayer##1"{HTTP.ExceptionRequest.var"#exceptions#exceptionlayer##0"{HTTP.ExceptionRequest.var"#exceptions#1#exceptionlayer##1"{typeof(HTTP.StreamRequest.streamlayer)}}}}}})(req::HTTP.Messages.Request; proxy::Nothing, socket_type::Type, socket_type_tls::Nothing, readtimeout::Int64, connect_timeout::Int64, logerrors::Bool, logtag::Nothing, closeimmediately::Bool, kw::@Kwargs{iofunction::Nothing, decompress::Nothing, verbose::Int64}) │ @ HTTP.ConnectionRequest ~/.julia/packages/HTTP/4AUPl/src/clientlayers/ConnectionRequest.jl:88 │ [2] connections │ @ ~/.julia/packages/HTTP/4AUPl/src/clientlayers/ConnectionRequest.jl:60 [inlined] │ [3] (::Base.var"#46#47"{Base.var"#48#49"{ExponentialBackOff, HTTP.RetryRequest.var"#retrylayer##2#retrylayer##3"{Int64, typeof(HTTP.RetryRequest.FALSE), HTTP.Messages.Request, Base.RefValue{Int64}}, HTTP.ConnectionRequest.var"#connections#connectionlayer##0"{HTTP.ConnectionRequest.var"#connections#1#connectionlayer##1"{HTTP.TimeoutRequest.var"#timeouts#timeoutlayer##0"{HTTP.TimeoutRequest.var"#timeouts#1#timeoutlayer##1"{HTTP.ExceptionRequest.var"#exceptions#exceptionlayer##0"{HTTP.ExceptionRequest.var"#exceptions#1#exceptionlayer##1"{typeof(HTTP.StreamRequest.streamlayer)}}}}}}}})(args::HTTP.Messages.Request; kwargs::@Kwargs{iofunction::Nothing, decompress::Nothing, verbose::Int64}) │ @ Base ./error.jl:322 │ [4] (::HTTP.RetryRequest.var"#manageretries#retrylayer##0"{HTTP.RetryRequest.var"#manageretries#1#retrylayer##1"{HTTP.ConnectionRequest.var"#connections#connectionlayer##0"{HTTP.ConnectionRequest.var"#connections#1#connectionlayer##1"{HTTP.TimeoutRequest.var"#timeouts#timeoutlayer##0"{HTTP.TimeoutRequest.var"#timeouts#1#timeoutlayer##1"{HTTP.ExceptionRequest.var"#exceptions#exceptionlayer##0"{HTTP.ExceptionRequest.var"#exceptions#1#exceptionlayer##1"{typeof(HTTP.StreamRequest.streamlayer)}}}}}}}})(req::HTTP.Messages.Request; retry::Bool, retries::Int64, retry_delays::ExponentialBackOff, retry_check::Function, retry_non_idempotent::Bool, kw::@Kwargs{iofunction::Nothing, decompress::Nothing, verbose::Int64}) │ @ HTTP.RetryRequest ~/.julia/packages/HTTP/4AUPl/src/clientlayers/RetryRequest.jl:75 │ [5] manageretries │ @ ~/.julia/packages/HTTP/4AUPl/src/clientlayers/RetryRequest.jl:30 [inlined] │ [6] (::HTTP.CookieRequest.var"#managecookies#cookielayer##0"{HTTP.CookieRequest.var"#managecookies#1#cookielayer##1"{HTTP.RetryRequest.var"#manageretries#retrylayer##0"{HTTP.RetryRequest.var"#manageretries#1#retrylayer##1"{HTTP.ConnectionRequest.var"#connections#connectionlayer##0"{HTTP.ConnectionRequest.var"#connections#1#connectionlayer##1"{HTTP.TimeoutRequest.var"#timeouts#timeoutlayer##0"{HTTP.TimeoutRequest.var"#timeouts#1#timeoutlayer##1"{HTTP.ExceptionRequest.var"#exceptions#exceptionlayer##0"{HTTP.ExceptionRequest.var"#exceptions#1#exceptionlayer##1"{typeof(HTTP.StreamRequest.streamlayer)}}}}}}}}}})(req::HTTP.Messages.Request; cookies::Bool, cookiejar::HTTP.Cookies.CookieJar, kw::@Kwargs{iofunction::Nothing, decompress::Nothing, verbose::Int64}) │ @ HTTP.CookieRequest ~/.julia/packages/HTTP/4AUPl/src/clientlayers/CookieRequest.jl:42 │ [7] managecookies │ @ ~/.julia/packages/HTTP/4AUPl/src/clientlayers/CookieRequest.jl:19 [inlined] │ [8] (::HTTP.HeadersRequest.var"#defaultheaders#headerslayer##0"{HTTP.HeadersRequest.var"#defaultheaders#1#headerslayer##1"{HTTP.CookieRequest.var"#managecookies#cookielayer##0"{HTTP.CookieRequest.var"#managecookies#1#cookielayer##1"{HTTP.RetryRequest.var"#manageretries#retrylayer##0"{HTTP.RetryRequest.var"#manageretries#1#retrylayer##1"{HTTP.ConnectionRequest.var"#connections#connectionlayer##0"{HTTP.ConnectionRequest.var"#connections#1#connectionlayer##1"{HTTP.TimeoutRequest.var"#timeouts#timeoutlayer##0"{HTTP.TimeoutRequest.var"#timeouts#1#timeoutlayer##1"{HTTP.ExceptionRequest.var"#exceptions#exceptionlayer##0"{HTTP.ExceptionRequest.var"#exceptions#1#exceptionlayer##1"{typeof(HTTP.StreamRequest.streamlayer)}}}}}}}}}}}})(req::HTTP.Messages.Request; iofunction::Nothing, decompress::Nothing, basicauth::Bool, detect_content_type::Bool, canonicalize_headers::Bool, kw::@Kwargs{verbose::Int64}) │ @ HTTP.HeadersRequest ~/.julia/packages/HTTP/4AUPl/src/clientlayers/HeadersRequest.jl:71 │ [9] defaultheaders │ @ ~/.julia/packages/HTTP/4AUPl/src/clientlayers/HeadersRequest.jl:14 [inlined] │ [10] (::HTTP.RedirectRequest.var"#redirects#redirectlayer##0"{HTTP.RedirectRequest.var"#redirects#1#redirectlayer##1"{HTTP.HeadersRequest.var"#defaultheaders#headerslayer##0"{HTTP.HeadersRequest.var"#defaultheaders#1#headerslayer##1"{HTTP.CookieRequest.var"#managecookies#cookielayer##0"{HTTP.CookieRequest.var"#managecookies#1#cookielayer##1"{HTTP.RetryRequest.var"#manageretries#retrylayer##0"{HTTP.RetryRequest.var"#manageretries#1#retrylayer##1"{HTTP.ConnectionRequest.var"#connections#connectionlayer##0"{HTTP.ConnectionRequest.var"#connections#1#connectionlayer##1"{HTTP.TimeoutRequest.var"#timeouts#timeoutlayer##0"{HTTP.TimeoutRequest.var"#timeouts#1#timeoutlayer##1"{HTTP.ExceptionRequest.var"#exceptions#exceptionlayer##0"{HTTP.ExceptionRequest.var"#exceptions#1#exceptionlayer##1"{typeof(HTTP.StreamRequest.streamlayer)}}}}}}}}}}}}}})(req::HTTP.Messages.Request; redirect::Bool, redirect_limit::Int64, redirect_method::Nothing, forwardheaders::Bool, response_stream::Nothing, kw::@Kwargs{verbose::Int64}) │ @ HTTP.RedirectRequest ~/.julia/packages/HTTP/4AUPl/src/clientlayers/RedirectRequest.jl:25 │ [11] redirects │ @ ~/.julia/packages/HTTP/4AUPl/src/clientlayers/RedirectRequest.jl:14 [inlined] │ [12] (::HTTP.MessageRequest.var"#makerequest#messagelayer##0"{HTTP.MessageRequest.var"#makerequest#1#messagelayer##1"{HTTP.RedirectRequest.var"#redirects#redirectlayer##0"{HTTP.RedirectRequest.var"#redirects#1#redirectlayer##1"{HTTP.HeadersRequest.var"#defaultheaders#headerslayer##0"{HTTP.HeadersRequest.var"#defaultheaders#1#headerslayer##1"{HTTP.CookieRequest.var"#managecookies#cookielayer##0"{HTTP.CookieRequest.var"#managecookies#1#cookielayer##1"{HTTP.RetryRequest.var"#manageretries#retrylayer##0"{HTTP.RetryRequest.var"#manageretries#1#retrylayer##1"{HTTP.ConnectionRequest.var"#connections#connectionlayer##0"{HTTP.ConnectionRequest.var"#connections#1#connectionlayer##1"{HTTP.TimeoutRequest.var"#timeouts#timeoutlayer##0"{HTTP.TimeoutRequest.var"#timeouts#1#timeoutlayer##1"{HTTP.ExceptionRequest.var"#exceptions#exceptionlayer##0"{HTTP.ExceptionRequest.var"#exceptions#1#exceptionlayer##1"{typeof(HTTP.StreamRequest.streamlayer)}}}}}}}}}}}}}}}})(method::String, url::URIs.URI, headers::Nothing, body::Vector{UInt8}; copyheaders::Bool, response_stream::Nothing, http_version::HTTP.Strings.HTTPVersion, verbose::Int64, kw::@Kwargs{}) │ @ HTTP.MessageRequest ~/.julia/packages/HTTP/4AUPl/src/clientlayers/MessageRequest.jl:35 │ [13] makerequest │ @ ~/.julia/packages/HTTP/4AUPl/src/clientlayers/MessageRequest.jl:24 [inlined] │ [14] request(stack::HTTP.MessageRequest.var"#makerequest#messagelayer##0"{HTTP.MessageRequest.var"#makerequest#1#messagelayer##1"{HTTP.RedirectRequest.var"#redirects#redirectlayer##0"{HTTP.RedirectRequest.var"#redirects#1#redirectlayer##1"{HTTP.HeadersRequest.var"#defaultheaders#headerslayer##0"{HTTP.HeadersRequest.var"#defaultheaders#1#headerslayer##1"{HTTP.CookieRequest.var"#managecookies#cookielayer##0"{HTTP.CookieRequest.var"#managecookies#1#cookielayer##1"{HTTP.RetryRequest.var"#manageretries#retrylayer##0"{HTTP.RetryRequest.var"#manageretries#1#retrylayer##1"{HTTP.ConnectionRequest.var"#connections#connectionlayer##0"{HTTP.ConnectionRequest.var"#connections#1#connectionlayer##1"{HTTP.TimeoutRequest.var"#timeouts#timeoutlayer##0"{HTTP.TimeoutRequest.var"#timeouts#1#timeoutlayer##1"{HTTP.ExceptionRequest.var"#exceptions#exceptionlayer##0"{HTTP.ExceptionRequest.var"#exceptions#1#exceptionlayer##1"{typeof(HTTP.StreamRequest.streamlayer)}}}}}}}}}}}}}}}}, method::String, url::String, h::Nothing, b::Vector{UInt8}, q::Nothing; headers::Nothing, body::Vector{UInt8}, query::Nothing, kw::@Kwargs{}) │ @ HTTP ~/.julia/packages/HTTP/4AUPl/src/HTTP.jl:457 │ [15] request(stack::Function, method::String, url::String, h::Nothing, b::Vector{UInt8}, q::Nothing) │ @ HTTP ~/.julia/packages/HTTP/4AUPl/src/HTTP.jl:455 │ [16] #request#21 │ @ ~/.julia/packages/HTTP/4AUPl/src/HTTP.jl:315 [inlined] │ [17] request (repeats 2 times) │ @ ~/.julia/packages/HTTP/4AUPl/src/HTTP.jl:313 [inlined] │ [18] get │ @ ~/.julia/packages/HTTP/4AUPl/src/HTTP.jl:518 [inlined] │ [19] macro expansion │ @ ~/.julia/packages/HTTP/4AUPl/src/precompile.jl:36 [inlined] │ [20] macro expansion │ @ ~/.julia/packages/PrecompileTools/L8A3n/src/workloads.jl:78 [inlined] │ [21] (::HTTP.var"#51#52"{String})() │ @ HTTP ~/.julia/packages/HTTP/4AUPl/src/precompile.jl:35 │ [22] withenv(::HTTP.var"#51#52"{String}, ::Pair{String, Union{Nothing, String}}, ::Vararg{Pair{String, Union{Nothing, String}}}) │ @ Base ./env.jl:265 │ [23] macro expansion │ @ ~/.julia/packages/HTTP/4AUPl/src/precompile.jl:34 [inlined] │ [24] macro expansion │ @ ~/.julia/packages/PrecompileTools/L8A3n/src/workloads.jl:140 [inlined] │ [25] top-level scope │ @ ~/.julia/packages/HTTP/4AUPl/src/precompile.jl:4 │ [26] include(mapexpr::Function, mod::Module, _path::String) │ @ Base ./Base.jl:301 │ [27] IncludeInto │ @ ./Base.jl:302 [inlined] │ [28] top-level scope │ @ ~/.julia/packages/HTTP/4AUPl/src/HTTP.jl:636 │ [29] include(mod::Module, _path::String) │ @ Base ./Base.jl:300 │ [30] 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::String) │ @ Base ./loading.jl:2995 │ [31] top-level scope │ @ stdin:6 │ [32] eval(m::Module, e::Any) │ @ Core ./boot.jl:485 │ [33] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) │ @ Base ./loading.jl:2846 │ [34] include_string │ @ ./loading.jl:2856 [inlined] │ [35] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:327 │ [36] _start() └ @ Base ./client.jl:558 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/8a0f840ec3a4b7913b278fad357755c65b097456/bin/git rev-parse --show-toplevel`,["PATH=/home/pkgeval/.julia/artifacts/96bc7b9ddb319d1a051535c85184aa2bf42dbd8b/bin:/home/pkgeval/.julia/artifacts/8be4b2d49ed77db4f9607e5f8a7b09cc105be2ee/bin:/home/pkgeval/.julia/artifacts/8a0f840ec3a4b7913b278fad357755c65b097456/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/4.3", "R_PDFVIEWER=", "LD_LIBRARY_PATH=/opt/julia/bin/../lib/julia:/home/pkgeval/.julia/artifacts/96bc7b9ddb319d1a051535c85184aa2bf42dbd8b/lib:/home/pkgeval/.julia/artifacts/8be4b2d49ed77db4f9607e5f8a7b09cc105be2ee/lib:/home/pkgeval/.julia/artifacts/5acd766faaca59c3c1f3cfa67e2bf6dcf1e3e883/lib:/opt/julia/bin/../lib/julia:/opt/julia/bin/../lib", "R_INCLUDE_DIR=/home/pkgeval/.julia/conda/3/x86_64/lib/R/include", "R_TEXI2DVICMD=/workspace/croot/r-base_1695428141831/_build_env/bin/texi2dvi", "R_HOME=/home/pkgeval/.julia/conda/3/x86_64/lib/R", "R_BZIPCMD=/home/pkgeval/.julia/conda/3/x86_64/bin/bzip2", "SED=/usr/bin/sed", "GIT_TEMPLATE_DIR=/home/pkgeval/.julia/artifacts/8a0f840ec3a4b7913b278fad357755c65b097456/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", "HOME=/home/pkgeval", "R_STRIP_STATIC_LIB=x86_64-conda-linux-gnu-strip --strip-debug", "JULIA_PKGEVAL=true", "PYTHON=", "R_GZIPCMD=gzip", "GIT_EXEC_PATH=/home/pkgeval/.julia/artifacts/8a0f840ec3a4b7913b278fad357755c65b097456/libexec/git-core", "MAKE=make", "R_SESSION_TMPDIR=/tmp/RtmpvigUw6", "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_SYSTEM_ABI=linux,gcc,gxx,gfortran,gfortran", "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_SIxBsW", "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:1137 [5] top-level scope @ ~/.julia/packages/Diversity/trAoz/test/clean_ResearchSoftwareMetadata.jl:33 [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1724 [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:301 [9] top-level scope @ ~/.julia/packages/Diversity/trAoz/test/runtests.jl:150 [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1724 [inlined] [11] macro expansion @ ~/.julia/packages/Diversity/trAoz/test/runtests.jl:155 [inlined] [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1813 [inlined] [13] macro expansion @ ~/.julia/packages/Diversity/trAoz/test/runtests.jl:158 [inlined] [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:301 [15] top-level scope @ none:6 [16] eval(m::Module, e::Any) @ Core ./boot.jl:485 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:295 [18] _start() @ Base ./client.jl:558 Test Summary: | Error Total Time test set | 2 2 1m59.6s c = JuliaFormatter | 1 1 1m03.6s JuliaFormatter | 1 1 6.1s c = ResearchSoftwareMetadata | 1 1 56.0s RSMD | 1 1 1.3s 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 1036.4s 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{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/v1.12/Pkg/src/Operations.jl:2359 [3] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2214 [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/v1.12/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/v1.12/Pkg/src/API.jl:159 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:147 [7] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:147 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:146 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [10] include(mod::Module, _path::String) @ Base ./Base.jl:300 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:329 [12] _start() @ Base ./client.jl:558 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1678.35s: networking-related issues were detected