Package evaluation of RCall on Julia 1.12.0-rc2.1 (084dab1917*) started at 2025-09-12T10:04:25.282 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.0s ################################################################################ # Installation # Installing RCall... Resolving package versions... Installed Conda ─ v1.10.2 Installed RCall ─ v0.14.9 Updating `~/.julia/environments/v1.12/Project.toml` [6f49c342] + RCall v0.14.9 Updating `~/.julia/environments/v1.12/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [324d7699] + CategoricalArrays v1.0.1 [34da2185] + Compat v4.18.0 [8f4d0f93] + Conda v1.10.2 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.0 ⌅ [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [ffbed154] + DocStringExtensions v0.9.5 [34004b35] + HypergeometricFunctions v0.3.28 [842dd82b] + InlineStrings v1.4.5 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [682c06a0] + JSON v0.21.4 [b964fa9f] + LaTeXStrings v1.4.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.3 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [08abe8d2] + PrettyTables v3.0.8 [43287f4e] + PtrArrays v1.3.0 [6f49c342] + RCall v0.14.9 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.8.0 [91c51154] + SentinelArrays v1.4.8 [1277b4bf] + ShiftedArrays v2.0.0 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.5.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.6 [4c63d2b9] + StatsFuns v1.5.0 [3eaba693] + StatsModels v0.7.6 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [81def892] + VersionParsing v1.3.0 [1b915085] + WinReg v1.0.0 [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 [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [b27032c2] + LibCURL v0.6.4 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [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 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.12.0 [f489334b] + StyledStrings v1.11.0 [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.11.1+1 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.5.20 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.1+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+1 [8e850ede] + nghttp2_jll v1.64.0+1 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Building Conda → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/b19db3927f0db4151cb86d073689f2428e524576/build.log` Building RCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/7521292e0ca900751cf0f35f2a2faf1cb321e960/build.log` Installation completed after 84.33s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 37.03s ################################################################################ # Testing # Testing RCall Status `/tmp/jl_yl2cSN/Project.toml` [39de3d68] AxisArrays v0.4.8 [324d7699] CategoricalArrays v1.0.1 [8f4d0f93] Conda v1.10.2 [992eb4ea] CondaPkg v0.2.31 [a93c6f00] DataFrames v1.8.0 ⌅ [864edb3b] DataStructures v0.18.22 [7073ff75] IJulia v1.30.4 [21216c6a] Preferences v1.5.0 [6f49c342] RCall v0.14.9 [3eaba693] StatsModels v0.7.6 [98d24dd4] TestSetExtensions v3.0.0 [44d3d7a6] Weave v0.10.12 [1b915085] WinReg v1.0.0 [ade2ca70] Dates v1.11.0 [8f399da3] Libdl v1.11.0 [56ddb016] Logging v1.11.0 [44cfe95a] Pkg v1.12.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_yl2cSN/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [39de3d68] AxisArrays v0.4.8 [324d7699] CategoricalArrays v1.0.1 [34da2185] Compat v4.18.0 [8f4d0f93] Conda v1.10.2 [992eb4ea] CondaPkg v0.2.31 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.0 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [ab62b9b5] DeepDiffs v1.2.0 [ffbed154] DocStringExtensions v0.9.5 [eafb193a] Highlights v0.5.3 [34004b35] HypergeometricFunctions v0.3.28 [7073ff75] IJulia v1.30.4 [842dd82b] InlineStrings v1.4.5 [8197267c] IntervalSets v0.7.11 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [c8e1da08] IterTools v1.10.0 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [682c06a0] JSON v0.21.4 [0f8b85d8] JSON3 v1.14.3 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [0b3b1443] MicroMamba v0.1.14 [e1d29d7a] Missings v1.2.0 [ffc61752] Mustache v1.0.21 [bac558e1] OrderedCollections v1.8.1 [69de0a69] Parsers v2.8.3 [fa939f87] Pidfile v1.3.0 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.0.8 [43287f4e] PtrArrays v1.3.0 [6f49c342] RCall v0.14.9 [b3c3ace0] RangeArrays v0.3.2 [189a3867] Reexport v1.2.2 [05181044] RelocatableFolders v1.0.1 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.8.0 [6c6a2e73] Scratch v1.3.0 [91c51154] SentinelArrays v1.4.8 [1277b4bf] ShiftedArrays v2.0.0 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.5.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.6 [4c63d2b9] StatsFuns v1.5.0 [3eaba693] StatsModels v0.7.6 [69024149] StringEncodings v0.3.7 [892a3eda] StringManipulation v0.4.1 [856f2bd8] StructTypes v1.11.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [98d24dd4] TestSetExtensions v3.0.0 [81def892] VersionParsing v1.3.0 [44d3d7a6] Weave v0.10.12 [1b915085] WinReg v1.0.0 [ddb6d928] YAML v0.4.14 [c2297ded] ZMQ v1.4.1 [94ce4f54] Libiconv_jll v1.18.0+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [8f1865be] ZeroMQ_jll v4.3.6+0 [a9144af2] libsodium_jll v1.0.21+0 ⌅ [f8abcde7] micromamba_jll v1.5.12+0 [4d7b5844] pixi_jll v0.41.3+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.12.0 [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 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.12.0 [f489334b] StyledStrings v1.11.0 [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.11.1+1 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.5.20 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.1+0 [bea87d4a] SuiteSparse_jll v7.8.3+2 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+1 [8e850ede] nghttp2_jll v1.64.0+1 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ..... Test Summary: | Pass Total Time installation | 5 5 13.5s ┌ Info: └ R_PPSTACKTOP_INITIAL = 8589934592 ┌ Warning: RCall.jl: Warning: Your system is mis-configured: ‘/var/db/timezone/localtime’ is not a symlink │ Warning: ‘/var/db/timezone/localtime’ is not identical to any known timezone file └ @ RCall ~/.julia/packages/RCall/GLHIY/src/io.jl:171 RObject{VecSxp} R version 4.5.1 (2025-06-13) Platform: x86_64-conda-linux-gnu Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default BLAS/LAPACK: /home/pkgeval/.julia/conda/3/x86_64/lib/libopenblasp-r0.3.29.so; LAPACK version 3.12.0 locale: [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C [3] LC_TIME=C.UTF-8 LC_COLLATE=C.UTF-8 [5] LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 [7] LC_PAPER=C.UTF-8 LC_NAME=C.UTF-8 [9] LC_ADDRESS=C.UTF-8 LC_TELEPHONE=C.UTF-8 [11] LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C.UTF-8 time zone: NA tzcode source: system (glibc) attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.5.1 RObject{VecSxp} $MBCS [1] TRUE $`UTF-8` [1] TRUE $`Latin-1` [1] FALSE $codeset [1] "UTF-8" ..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................┌ Warning: RCall.jl: Loading required package: MASS │ Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : │ there is no package called ‘MASS’ └ @ RCall ~/.julia/packages/RCall/GLHIY/src/io.jl:171 ┌ Info: └ has_mass_package = false ┌ 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/GLHIY/src/io.jl:171 [ Info: installing ape to temporary lib sh: 1: wget: not found sh: 1: wget: not found sh: 1: wget: not found ┌ Warning: RCall.jl: Warning: unable to access index for repository https://cloud.r-project.org/src/contrib: │ 'wget' call had nonzero exit status │ Warning: package ‘ape’ is not available for this version of R │ │ A version of this package for your version of R might be available elsewhere, │ see the ideas at │ https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages └ @ RCall ~/.julia/packages/RCall/GLHIY/src/io.jl:171 ===================================================== namespaces: Error During Test at /home/pkgeval/.julia/packages/RCall/GLHIY/test/runtests.jl:71 Got exception outside of a @test LoadError: REvalError: Error in library("ape") : there is no package called ‘ape’ Stacktrace: [1] handle_eval_stderr(; as_warning::Bool) @ RCall ~/.julia/packages/RCall/GLHIY/src/io.jl:173 [2] handle_eval_stderr @ ~/.julia/packages/RCall/GLHIY/src/io.jl:167 [inlined] [3] reval_p(expr::Ptr{LangSxp}, env::Ptr{EnvSxp}) @ RCall ~/.julia/packages/RCall/GLHIY/src/eval.jl:103 [4] reval_p(expr::Ptr{RCall.ExprSxp}, env::Ptr{EnvSxp}) @ RCall ~/.julia/packages/RCall/GLHIY/src/eval.jl:119 [5] reval(str::String, env::RObject{EnvSxp}) @ RCall ~/.julia/packages/RCall/GLHIY/src/eval.jl:136 [6] reval(str::String) @ RCall ~/.julia/packages/RCall/GLHIY/src/eval.jl:136 [7] top-level scope @ ~/.julia/packages/RCall/GLHIY/test/namespaces.jl:30 [8] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [9] top-level scope @ ~/.julia/packages/RCall/GLHIY/test/runtests.jl:72 [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [11] macro expansion @ ~/.julia/packages/RCall/GLHIY/test/runtests.jl:72 [inlined] [12] eval(m::Module, e::Any) @ Core ./boot.jl:489 [13] macro expansion @ ~/.julia/packages/RCall/GLHIY/test/runtests.jl:71 [inlined] [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [15] top-level scope @ ~/.julia/packages/RCall/GLHIY/test/runtests.jl:48 [16] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [17] top-level scope @ none:6 [18] eval(m::Module, e::Any) @ Core ./boot.jl:489 [19] exec_options(opts::Base.JLOptions) @ Base ./client.jl:287 [20] _start() @ Base ./client.jl:554 in expression starting at /home/pkgeval/.julia/packages/RCall/GLHIY/test/namespaces.jl:5 ===================================================== .....┌ Error: Error in the keymap │ exception = │ MethodError: no method matching _completion_text(::REPL.REPLCompletions.BslashCompletion) │ The function `_completion_text` exists, but no method is defined for this combination of argument types. │ │ Closest candidates are: │ _completion_text(!Matched::REPL.REPLCompletions.PackageCompletion) │ @ REPL /opt/julia/share/julia/stdlib/v1.12/REPL/src/REPLCompletions.jl:119 │ _completion_text(!Matched::REPL.REPLCompletions.MethodCompletion) │ @ REPL /opt/julia/share/julia/stdlib/v1.12/REPL/src/REPLCompletions.jl:122 │ _completion_text(!Matched::REPL.REPLCompletions.PropertyCompletion) │ @ REPL /opt/julia/share/julia/stdlib/v1.12/REPL/src/REPLCompletions.jl:120 │ ... │ │ Stacktrace: │ [1] completion_text(c::REPL.REPLCompletions.BslashCompletion) │ @ REPL.REPLCompletions /opt/julia/share/julia/stdlib/v1.12/REPL/src/REPLCompletions.jl:127 │ [2] iterate │ @ ./generator.jl:48 [inlined] │ [3] _collect(c::Vector{REPL.REPLCompletions.Completion}, itr::Base.Generator{Vector{REPL.REPLCompletions.Completion}, typeof(REPL.REPLCompletions.completion_text)}, ::Base.EltypeUnknown, isz::Base.HasShape{1}) │ @ Base ./array.jl:810 │ [4] collect_similar │ @ ./array.jl:732 [inlined] │ [5] map │ @ ./abstractarray.jl:3372 [inlined] │ [6] complete_line(c::RCall.RPrompt.RCompletionProvider, s::REPL.LineEdit.PromptState; hint::Bool) │ @ RCall.RPrompt ~/.julia/packages/RCall/GLHIY/src/RPrompt.jl:155 │ [7] complete_line(c::REPL.LineEdit.CompletionProvider, s::Any, ::Module; hint::Bool) │ @ REPL.LineEdit /opt/julia/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:202 │ [8] complete_line_named(c::Any, s::Any, args::Any; kwargs...) │ @ REPL.LineEdit /opt/julia/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:401 │ [9] complete_line_named │ @ /opt/julia/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:400 [inlined] │ [10] complete_line(s::REPL.LineEdit.PromptState, repeats::Int64, mod::Module; hint::Bool) │ @ REPL.LineEdit /opt/julia/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:497 │ [11] complete_line(s::REPL.LineEdit.PromptState, repeats::Int64, mod::Module) │ @ REPL.LineEdit /opt/julia/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:496 │ [12] complete_line(s::REPL.LineEdit.MIState) │ @ REPL.LineEdit /opt/julia/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:386 │ [13] edit_tab(s::REPL.LineEdit.MIState, jump_spaces::Bool, delete_trailing::Bool) │ @ REPL.LineEdit /opt/julia/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:2518 │ [14] edit_tab │ @ /opt/julia/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:2518 [inlined] │ [15] (::REPL.LineEdit.var"#141#142")(::REPL.LineEdit.MIState, ::Any, ::Vararg{Any}) │ @ REPL.LineEdit /opt/julia/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:2564 │ [16] (::REPL.LineEdit.var"#match_input##0#match_input##1"{REPL.LineEdit.var"#141#142", String})(s::Any, p::Any) │ @ REPL.LineEdit /opt/julia/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:1810 │ [17] macro expansion │ @ /opt/julia/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:2960 [inlined] │ [18] macro expansion │ @ ./lock.jl:376 [inlined] │ [19] (::REPL.LineEdit.var"#prompt!##2#prompt!##3"{FakeTerminal, REPL.LineEdit.ModalInterface, REPL.LineEdit.MIState, REPL.LineEdit.Prompt})() │ @ REPL.LineEdit /opt/julia/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:2949 └ @ REPL.LineEdit /opt/julia/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:2962 ===================================================== repl: Error During Test at /home/pkgeval/.julia/packages/RCall/GLHIY/test/repl.jl:71 Test threw exception Expression: check_repl_stdout("\\alpha") TaskFailedException Stacktrace: [1] #wait#582 @ ./task.jl:363 [inlined] [2] wait @ ./task.jl:360 [inlined] [3] fetch @ ./task.jl:525 [inlined] [4] read_repl(io::Pipe, x::String) @ Main ~/.julia/packages/RCall/GLHIY/test/repl.jl:42 [5] check_repl_stdout(x::String) @ Main ~/.julia/packages/RCall/GLHIY/test/repl.jl:47 [6] top-level scope @ ~/.julia/packages/RCall/GLHIY/test/repl.jl:516 [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:677 [inlined] [8] macro expansion @ ~/.julia/packages/RCall/GLHIY/test/repl.jl:71 [inlined] nested task error: Expect "\alpha", but wait too long. Stacktrace: [1] try_yieldto(undo::typeof(Base.ensure_rescheduled)) @ Base ./task.jl:1128 [2] wait() @ Base ./task.jl:1200 [3] wait(c::Base.GenericCondition{Base.Threads.SpinLock}; first::Bool) @ Base ./condition.jl:141 [4] wait @ ./condition.jl:136 [inlined] [5] wait_readnb(x::Base.PipeEndpoint, nb::Int64) @ Base ./stream.jl:416 [6] eof @ ./stream.jl:106 [inlined] [7] iterate @ ./io.jl:1381 [inlined] [8] readuntil_vector!(io::Base.PipeEndpoint, target::Base.CodeUnits{UInt8, String}, keep::Bool, out::IOBuffer) @ Base ./io.jl:1084 [9] copyuntil @ ./io.jl:1117 [inlined] [10] copyuntil(out::IOBuffer, io::Base.PipeEndpoint, target::String; keep::Bool) @ Base ./io.jl:1109 [11] copyuntil @ ./io.jl:1096 [inlined] [12] copyuntil @ ./io.jl:466 [inlined] [13] readuntil(stream::Pipe, delim::String; kw::@Kwargs{}) @ Base ./io.jl:547 [14] readuntil @ ./io.jl:547 [inlined] [15] (::var"#read_repl##0#read_repl##1"{Pipe, String, Base.RefValue{Any}})() @ Main ~/.julia/packages/RCall/GLHIY/test/repl.jl:38 ===================================================== ===================================================== repl: Error During Test at /home/pkgeval/.julia/packages/RCall/GLHIY/test/repl.jl:74 Test threw exception Expression: check_repl_stdout("α") TaskFailedException Stacktrace: [1] #wait#582 @ ./task.jl:363 [inlined] [2] wait @ ./task.jl:360 [inlined] [3] fetch @ ./task.jl:525 [inlined] [4] read_repl(io::Pipe, x::String) @ Main ~/.julia/packages/RCall/GLHIY/test/repl.jl:42 [5] check_repl_stdout(x::String) @ Main ~/.julia/packages/RCall/GLHIY/test/repl.jl:47 [6] top-level scope @ ~/.julia/packages/RCall/GLHIY/test/repl.jl:516 [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:677 [inlined] [8] macro expansion @ ~/.julia/packages/RCall/GLHIY/test/repl.jl:74 [inlined] nested task error: Expect "α", but wait too long. Stacktrace: [1] try_yieldto(undo::typeof(Base.ensure_rescheduled)) @ Base ./task.jl:1128 [2] wait() @ Base ./task.jl:1200 [3] wait(c::Base.GenericCondition{Base.Threads.SpinLock}; first::Bool) @ Base ./condition.jl:141 [4] wait @ ./condition.jl:136 [inlined] [5] wait_readnb(x::Base.PipeEndpoint, nb::Int64) @ Base ./stream.jl:416 [6] eof @ ./stream.jl:106 [inlined] [7] iterate (repeats 2 times) @ ./io.jl:1381 [inlined] [8] readuntil_vector!(io::Base.PipeEndpoint, target::Base.CodeUnits{UInt8, String}, keep::Bool, out::IOBuffer) @ Base ./io.jl:1036 [9] copyuntil @ ./io.jl:1117 [inlined] [10] copyuntil(out::IOBuffer, io::Base.PipeEndpoint, target::String; keep::Bool) @ Base ./io.jl:1109 [11] copyuntil @ ./io.jl:1096 [inlined] [12] copyuntil @ ./io.jl:466 [inlined] [13] readuntil(stream::Pipe, delim::String; kw::@Kwargs{}) @ Base ./io.jl:547 [14] readuntil @ ./io.jl:547 [inlined] [15] (::var"#read_repl##0#read_repl##1"{Pipe, String, Base.RefValue{Any}})() @ Main ~/.julia/packages/RCall/GLHIY/test/repl.jl:38 ===================================================== ...............Precompiling packages... 5053.8 ms ✓ Mustache 10872.0 ms ✓ Weave 2 dependencies successfully precompiled in 17 seconds. 49 already precompiled. [ Info: Installing 'julia 1.12.0-rc2' kernelspec in /home/pkgeval/.local/share/jupyter/kernels/julia-1.12 [ Info: Running `conda install -q -y jupyter` in root environment Channels: - r - defaults - conda-forge Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/pkgeval/.julia/conda/3/x86_64 added / updated specs: - jupyter The following packages will be downloaded: package | build ---------------------------|----------------- alsa-lib-1.2.14 | h5eee18b_0 610 KB anyio-4.7.0 | py312h06a4308_0 263 KB argon2-cffi-21.3.0 | pyhd3eb1b0_0 15 KB argon2-cffi-bindings-21.2.0| py312h5eee18b_1 33 KB asttokens-3.0.0 | py312h06a4308_0 47 KB async-lru-2.0.4 | py312h06a4308_0 20 KB attr-2.5.2 | h39aace5_0 66 KB conda-forge attrs-24.3.0 | py312h06a4308_0 172 KB babel-2.16.0 | py312h06a4308_0 6.9 MB beautifulsoup4-4.13.5 | py312h06a4308_0 251 KB bleach-6.2.0 | py312h06a4308_0 362 KB comm-0.2.1 | py312h06a4308_0 16 KB cyrus-sasl-2.1.28 | h1110e0f_3 242 KB dbus-1.16.2 | h5bd4931_0 1.2 MB debugpy-1.8.16 | py312hbdd6827_0 2.6 MB decorator-5.2.1 | py312h06a4308_0 42 KB defusedxml-0.7.1 | pyhd3eb1b0_0 23 KB executing-2.2.1 | py312h06a4308_0 341 KB expat-2.7.1 | h6a678d5_0 182 KB gettext-0.25.1 | h3f43e3d_1 529 KB conda-forge gettext-tools-0.25.1 | h3f43e3d_1 3.5 MB conda-forge glib-2.86.0 | he175458_0 597 KB conda-forge glib-tools-2.86.0 | hf516916_0 115 KB conda-forge gst-plugins-base-1.24.11 | h651a532_0 2.7 MB conda-forge gstreamer-1.24.11 | hc37bda9_0 1.9 MB conda-forge h11-0.16.0 | py312h06a4308_0 63 KB httpcore-1.0.9 | py312h06a4308_0 123 KB httpx-0.28.1 | py312h06a4308_0 218 KB ipykernel-6.30.1 | py312h06a4308_0 243 KB ipython-9.1.0 | py312h06a4308_0 1.2 MB ipython_pygments_lexers-1.1.1| py312h06a4308_0 17 KB ipywidgets-8.1.5 | py312h06a4308_0 245 KB jedi-0.19.2 | py312h06a4308_0 1.2 MB jinja2-3.1.6 | py312h06a4308_0 352 KB json5-0.9.25 | py312h06a4308_0 53 KB jsonschema-4.25.0 | py312h06a4308_0 200 KB jsonschema-specifications-2023.7.1| py312h06a4308_0 15 KB jupyter-1.1.1 | py312h06a4308_0 8 KB jupyter-lsp-2.2.5 | py312h06a4308_0 114 KB jupyter_client-8.6.3 | py312h06a4308_0 231 KB jupyter_console-6.6.3 | py312h06a4308_1 52 KB jupyter_core-5.8.1 | py312h06a4308_0 95 KB jupyter_events-0.12.0 | py312h06a4308_0 42 KB jupyter_server-2.16.0 | py312h06a4308_0 596 KB jupyter_server_terminals-0.5.3| py312h06a4308_0 28 KB jupyterlab-4.4.6 | py312h06a4308_0 5.8 MB jupyterlab_pygments-0.3.0 | py312h06a4308_0 18 KB jupyterlab_server-2.27.3 | py312h06a4308_0 111 KB jupyterlab_widgets-3.0.15 | py312h06a4308_0 198 KB lame-3.100 | h7b6447c_0 323 KB libasprintf-0.25.1 | h3f43e3d_1 52 KB conda-forge libasprintf-devel-0.25.1 | h3f43e3d_1 34 KB conda-forge libcap-2.76 | h0b2e76d_0 119 KB conda-forge libclang-cpp20.1-20.1.8 |default_h4fcecc7_0 22.1 MB libclang13-20.1.8 |default_hee3e7a4_0 12.8 MB libcups-2.3.3 | hb8b1518_5 4.3 MB conda-forge libdrm-2.4.124 | h5eee18b_0 320 KB libegl-1.7.0 | h5eee18b_2 44 KB libevent-2.1.12 | hdbd6064_1 453 KB libflac-1.4.3 | h59595ed_0 385 KB conda-forge libgcrypt-lib-1.11.1 | hb9d3cd8_0 577 KB conda-forge libgettextpo-0.25.1 | h3f43e3d_1 184 KB conda-forge libgettextpo-devel-0.25.1 | h3f43e3d_1 37 KB conda-forge libgl-1.7.0 | h5eee18b_2 149 KB libglvnd-1.7.0 | h5eee18b_2 140 KB libglx-1.7.0 | h5eee18b_2 87 KB libgpg-error-1.55 | h3f2d84a_0 305 KB conda-forge libkrb5-1.21.3 | h520c7b4_4 874 KB libllvm20-20.1.8 | h465586c_0 45.3 MB libogg-1.3.5 | h27cfd23_1 199 KB libopus-1.5.2 | hd0c01bc_0 305 KB conda-forge libpciaccess-0.18 | h5eee18b_0 26 KB libpq-17.5 | h27ae623_0 2.6 MB conda-forge libsndfile-1.2.2 | hc60ed4a_1 346 KB conda-forge libsodium-1.0.18 | h7b6447c_0 244 KB libsystemd0-257.9 | h996ca69_0 481 KB conda-forge libvorbis-1.3.7 | h7b6447c_0 398 KB libxkbcommon-1.11.0 | he8b52b9_0 773 KB conda-forge lmdb-0.9.31 | hb25bd0a_0 469 KB markupsafe-3.0.2 | py312h5eee18b_0 26 KB matplotlib-inline-0.1.6 | py312h06a4308_0 18 KB mistune-3.1.2 | py312h06a4308_0 145 KB mpg123-1.32.9 | hc50e24c_0 480 KB conda-forge nbclient-0.10.2 | py312h06a4308_0 53 KB nbconvert-7.16.6 | py312h06a4308_0 7 KB nbconvert-core-7.16.6 | py312h06a4308_0 510 KB nbconvert-pandoc-7.16.6 | py312h06a4308_0 7 KB nbformat-5.10.4 | py312h06a4308_0 157 KB nest-asyncio-1.6.0 | py312h06a4308_0 16 KB notebook-7.4.5 | py312h06a4308_0 5.9 MB notebook-shim-0.2.4 | py312h06a4308_0 26 KB nspr-4.37 | h29cc59b_0 226 KB conda-forge nss-3.114 | hc3c8bcf_0 1.9 MB conda-forge openldap-2.6.10 | h8e75217_0 815 KB overrides-7.4.0 | py312h06a4308_0 36 KB pandoc-2.12 | h06a4308_3 10.5 MB pandocfilters-1.5.1 | py312h06a4308_0 17 KB parso-0.8.4 | py312h06a4308_0 233 KB pexpect-4.9.0 | py312h06a4308_0 157 KB ply-3.11 | py312h06a4308_1 109 KB prometheus_client-0.21.1 | py312h06a4308_0 151 KB prompt-toolkit-3.0.43 | py312h06a4308_0 732 KB prompt_toolkit-3.0.43 | hd3eb1b0_0 5 KB psutil-7.0.0 | py312hee96239_0 531 KB ptyprocess-0.7.0 | pyhd3eb1b0_2 17 KB pulseaudio-client-17.0 | h9a8bead_2 744 KB conda-forge pure_eval-0.2.3 | py312h06a4308_0 33 KB pygments-2.19.1 | py312h06a4308_0 2.2 MB pyqt-5.15.10 | py312h6a678d5_1 5.7 MB pyqt5-sip-12.13.0 | py312h5eee18b_1 96 KB python-dateutil-2.9.0post0 | py312h06a4308_2 318 KB python-fastjsonschema-2.20.0| py312h06a4308_0 260 KB python-json-logger-3.2.1 | py312h06a4308_0 27 KB pyyaml-6.0.2 | py312h5eee18b_0 217 KB pyzmq-26.2.0 | py312h6a678d5_0 387 KB qt-main-5.15.15 | hea1682b_4 50.1 MB conda-forge qtconsole-5.6.1 | py312h06a4308_1 264 KB qtpy-2.4.3 | py312h06a4308_0 127 KB referencing-0.30.2 | py312h06a4308_0 73 KB rfc3339-validator-0.1.4 | py312h06a4308_0 9 KB rfc3986-validator-0.1.1 | py312h06a4308_0 9 KB rpds-py-0.22.3 | py312h4aa5aa6_0 371 KB send2trash-1.8.2 | py312h06a4308_1 31 KB sip-6.7.12 | py312h6a678d5_1 598 KB six-1.17.0 | py312h06a4308_0 36 KB sniffio-1.3.0 | py312h06a4308_0 16 KB soupsieve-2.5 | py312h06a4308_0 84 KB stack_data-0.6.3 | py312h06a4308_0 65 KB terminado-0.17.1 | py312h06a4308_0 38 KB tinycss2-1.4.0 | py312h06a4308_0 109 KB tornado-6.5.1 | py312h5eee18b_0 875 KB traitlets-5.14.3 | py312h06a4308_0 219 KB typing-extensions-4.15.0 | py312h06a4308_0 11 KB typing_extensions-4.15.0 | py312h06a4308_0 99 KB wcwidth-0.2.13 | py312h06a4308_0 73 KB webencodings-0.5.1 | py312h06a4308_2 25 KB websocket-client-1.8.0 | py312h06a4308_0 116 KB widgetsnbextension-4.0.13 | py312h06a4308_0 969 KB xcb-util-0.4.1 | h5eee18b_2 19 KB xcb-util-image-0.4.0 | h5eee18b_2 23 KB xcb-util-keysyms-0.4.1 | h5eee18b_0 13 KB xcb-util-renderutil-0.3.10 | h5eee18b_0 16 KB xcb-util-wm-0.4.2 | h5eee18b_0 55 KB xkeyboard-config-2.44 | h5eee18b_0 411 KB xorg-libxdamage-1.1.6 | h9b100fa_0 12 KB xorg-libxfixes-6.0.1 | h9b100fa_0 18 KB xorg-libxshmfence-1.3.3 | h9b100fa_0 11 KB xorg-libxxf86vm-1.1.6 | h9b100fa_0 16 KB yaml-0.2.5 | h7b6447c_0 75 KB zeromq-4.3.5 | h6a678d5_0 366 KB ------------------------------------------------------------ Total: 215.8 MB The following NEW packages will be INSTALLED: alsa-lib pkgs/main/linux-64::alsa-lib-1.2.14-h5eee18b_0 anyio pkgs/main/linux-64::anyio-4.7.0-py312h06a4308_0 argon2-cffi pkgs/main/noarch::argon2-cffi-21.3.0-pyhd3eb1b0_0 argon2-cffi-bindi~ pkgs/main/linux-64::argon2-cffi-bindings-21.2.0-py312h5eee18b_1 asttokens pkgs/main/linux-64::asttokens-3.0.0-py312h06a4308_0 async-lru pkgs/main/linux-64::async-lru-2.0.4-py312h06a4308_0 attr conda-forge/linux-64::attr-2.5.2-h39aace5_0 attrs pkgs/main/linux-64::attrs-24.3.0-py312h06a4308_0 babel pkgs/main/linux-64::babel-2.16.0-py312h06a4308_0 beautifulsoup4 pkgs/main/linux-64::beautifulsoup4-4.13.5-py312h06a4308_0 bleach pkgs/main/linux-64::bleach-6.2.0-py312h06a4308_0 comm pkgs/main/linux-64::comm-0.2.1-py312h06a4308_0 cyrus-sasl pkgs/main/linux-64::cyrus-sasl-2.1.28-h1110e0f_3 dbus pkgs/main/linux-64::dbus-1.16.2-h5bd4931_0 debugpy pkgs/main/linux-64::debugpy-1.8.16-py312hbdd6827_0 decorator pkgs/main/linux-64::decorator-5.2.1-py312h06a4308_0 defusedxml pkgs/main/noarch::defusedxml-0.7.1-pyhd3eb1b0_0 executing pkgs/main/linux-64::executing-2.2.1-py312h06a4308_0 expat pkgs/main/linux-64::expat-2.7.1-h6a678d5_0 gettext conda-forge/linux-64::gettext-0.25.1-h3f43e3d_1 gettext-tools conda-forge/linux-64::gettext-tools-0.25.1-h3f43e3d_1 glib conda-forge/linux-64::glib-2.86.0-he175458_0 glib-tools conda-forge/linux-64::glib-tools-2.86.0-hf516916_0 gst-plugins-base conda-forge/linux-64::gst-plugins-base-1.24.11-h651a532_0 gstreamer conda-forge/linux-64::gstreamer-1.24.11-hc37bda9_0 h11 pkgs/main/linux-64::h11-0.16.0-py312h06a4308_0 httpcore pkgs/main/linux-64::httpcore-1.0.9-py312h06a4308_0 httpx pkgs/main/linux-64::httpx-0.28.1-py312h06a4308_0 ipykernel pkgs/main/linux-64::ipykernel-6.30.1-py312h06a4308_0 ipython pkgs/main/linux-64::ipython-9.1.0-py312h06a4308_0 ipython_pygments_~ pkgs/main/linux-64::ipython_pygments_lexers-1.1.1-py312h06a4308_0 ipywidgets pkgs/main/linux-64::ipywidgets-8.1.5-py312h06a4308_0 jedi pkgs/main/linux-64::jedi-0.19.2-py312h06a4308_0 jinja2 pkgs/main/linux-64::jinja2-3.1.6-py312h06a4308_0 json5 pkgs/main/linux-64::json5-0.9.25-py312h06a4308_0 jsonschema pkgs/main/linux-64::jsonschema-4.25.0-py312h06a4308_0 jsonschema-specif~ pkgs/main/linux-64::jsonschema-specifications-2023.7.1-py312h06a4308_0 jupyter pkgs/main/linux-64::jupyter-1.1.1-py312h06a4308_0 jupyter-lsp pkgs/main/linux-64::jupyter-lsp-2.2.5-py312h06a4308_0 jupyter_client pkgs/main/linux-64::jupyter_client-8.6.3-py312h06a4308_0 jupyter_console pkgs/main/linux-64::jupyter_console-6.6.3-py312h06a4308_1 jupyter_core pkgs/main/linux-64::jupyter_core-5.8.1-py312h06a4308_0 jupyter_events pkgs/main/linux-64::jupyter_events-0.12.0-py312h06a4308_0 jupyter_server pkgs/main/linux-64::jupyter_server-2.16.0-py312h06a4308_0 jupyter_server_te~ pkgs/main/linux-64::jupyter_server_terminals-0.5.3-py312h06a4308_0 jupyterlab pkgs/main/linux-64::jupyterlab-4.4.6-py312h06a4308_0 jupyterlab_pygmen~ pkgs/main/linux-64::jupyterlab_pygments-0.3.0-py312h06a4308_0 jupyterlab_server pkgs/main/linux-64::jupyterlab_server-2.27.3-py312h06a4308_0 jupyterlab_widgets pkgs/main/linux-64::jupyterlab_widgets-3.0.15-py312h06a4308_0 lame pkgs/main/linux-64::lame-3.100-h7b6447c_0 libasprintf conda-forge/linux-64::libasprintf-0.25.1-h3f43e3d_1 libasprintf-devel conda-forge/linux-64::libasprintf-devel-0.25.1-h3f43e3d_1 libcap conda-forge/linux-64::libcap-2.76-h0b2e76d_0 libclang-cpp20.1 pkgs/main/linux-64::libclang-cpp20.1-20.1.8-default_h4fcecc7_0 libclang13 pkgs/main/linux-64::libclang13-20.1.8-default_hee3e7a4_0 libcups conda-forge/linux-64::libcups-2.3.3-hb8b1518_5 libdrm pkgs/main/linux-64::libdrm-2.4.124-h5eee18b_0 libegl pkgs/main/linux-64::libegl-1.7.0-h5eee18b_2 libevent pkgs/main/linux-64::libevent-2.1.12-hdbd6064_1 libflac conda-forge/linux-64::libflac-1.4.3-h59595ed_0 libgcrypt-lib conda-forge/linux-64::libgcrypt-lib-1.11.1-hb9d3cd8_0 libgettextpo conda-forge/linux-64::libgettextpo-0.25.1-h3f43e3d_1 libgettextpo-devel conda-forge/linux-64::libgettextpo-devel-0.25.1-h3f43e3d_1 libgl pkgs/main/linux-64::libgl-1.7.0-h5eee18b_2 libglvnd pkgs/main/linux-64::libglvnd-1.7.0-h5eee18b_2 libglx pkgs/main/linux-64::libglx-1.7.0-h5eee18b_2 libgpg-error conda-forge/linux-64::libgpg-error-1.55-h3f2d84a_0 libkrb5 pkgs/main/linux-64::libkrb5-1.21.3-h520c7b4_4 libllvm20 pkgs/main/linux-64::libllvm20-20.1.8-h465586c_0 libogg pkgs/main/linux-64::libogg-1.3.5-h27cfd23_1 libopus conda-forge/linux-64::libopus-1.5.2-hd0c01bc_0 libpciaccess pkgs/main/linux-64::libpciaccess-0.18-h5eee18b_0 libpq conda-forge/linux-64::libpq-17.5-h27ae623_0 libsndfile conda-forge/linux-64::libsndfile-1.2.2-hc60ed4a_1 libsodium pkgs/main/linux-64::libsodium-1.0.18-h7b6447c_0 libsystemd0 conda-forge/linux-64::libsystemd0-257.9-h996ca69_0 libvorbis pkgs/main/linux-64::libvorbis-1.3.7-h7b6447c_0 libxkbcommon conda-forge/linux-64::libxkbcommon-1.11.0-he8b52b9_0 lmdb pkgs/main/linux-64::lmdb-0.9.31-hb25bd0a_0 markupsafe pkgs/main/linux-64::markupsafe-3.0.2-py312h5eee18b_0 matplotlib-inline pkgs/main/linux-64::matplotlib-inline-0.1.6-py312h06a4308_0 mistune pkgs/main/linux-64::mistune-3.1.2-py312h06a4308_0 mpg123 conda-forge/linux-64::mpg123-1.32.9-hc50e24c_0 nbclient pkgs/main/linux-64::nbclient-0.10.2-py312h06a4308_0 nbconvert pkgs/main/linux-64::nbconvert-7.16.6-py312h06a4308_0 nbconvert-core pkgs/main/linux-64::nbconvert-core-7.16.6-py312h06a4308_0 nbconvert-pandoc pkgs/main/linux-64::nbconvert-pandoc-7.16.6-py312h06a4308_0 nbformat pkgs/main/linux-64::nbformat-5.10.4-py312h06a4308_0 nest-asyncio pkgs/main/linux-64::nest-asyncio-1.6.0-py312h06a4308_0 notebook pkgs/main/linux-64::notebook-7.4.5-py312h06a4308_0 notebook-shim pkgs/main/linux-64::notebook-shim-0.2.4-py312h06a4308_0 nspr conda-forge/linux-64::nspr-4.37-h29cc59b_0 nss conda-forge/linux-64::nss-3.114-hc3c8bcf_0 openldap pkgs/main/linux-64::openldap-2.6.10-h8e75217_0 overrides pkgs/main/linux-64::overrides-7.4.0-py312h06a4308_0 pandoc pkgs/main/linux-64::pandoc-2.12-h06a4308_3 pandocfilters pkgs/main/linux-64::pandocfilters-1.5.1-py312h06a4308_0 parso pkgs/main/linux-64::parso-0.8.4-py312h06a4308_0 pexpect pkgs/main/linux-64::pexpect-4.9.0-py312h06a4308_0 ply pkgs/main/linux-64::ply-3.11-py312h06a4308_1 prometheus_client pkgs/main/linux-64::prometheus_client-0.21.1-py312h06a4308_0 prompt-toolkit pkgs/main/linux-64::prompt-toolkit-3.0.43-py312h06a4308_0 prompt_toolkit pkgs/main/noarch::prompt_toolkit-3.0.43-hd3eb1b0_0 psutil pkgs/main/linux-64::psutil-7.0.0-py312hee96239_0 ptyprocess pkgs/main/noarch::ptyprocess-0.7.0-pyhd3eb1b0_2 pulseaudio-client conda-forge/linux-64::pulseaudio-client-17.0-h9a8bead_2 pure_eval pkgs/main/linux-64::pure_eval-0.2.3-py312h06a4308_0 pygments pkgs/main/linux-64::pygments-2.19.1-py312h06a4308_0 pyqt pkgs/main/linux-64::pyqt-5.15.10-py312h6a678d5_1 pyqt5-sip pkgs/main/linux-64::pyqt5-sip-12.13.0-py312h5eee18b_1 python-dateutil pkgs/main/linux-64::python-dateutil-2.9.0post0-py312h06a4308_2 python-fastjsonsc~ pkgs/main/linux-64::python-fastjsonschema-2.20.0-py312h06a4308_0 python-json-logger pkgs/main/linux-64::python-json-logger-3.2.1-py312h06a4308_0 pyyaml pkgs/main/linux-64::pyyaml-6.0.2-py312h5eee18b_0 pyzmq pkgs/main/linux-64::pyzmq-26.2.0-py312h6a678d5_0 qt-main conda-forge/linux-64::qt-main-5.15.15-hea1682b_4 qtconsole pkgs/main/linux-64::qtconsole-5.6.1-py312h06a4308_1 qtpy pkgs/main/linux-64::qtpy-2.4.3-py312h06a4308_0 referencing pkgs/main/linux-64::referencing-0.30.2-py312h06a4308_0 rfc3339-validator pkgs/main/linux-64::rfc3339-validator-0.1.4-py312h06a4308_0 rfc3986-validator pkgs/main/linux-64::rfc3986-validator-0.1.1-py312h06a4308_0 rpds-py pkgs/main/linux-64::rpds-py-0.22.3-py312h4aa5aa6_0 send2trash pkgs/main/linux-64::send2trash-1.8.2-py312h06a4308_1 sip pkgs/main/linux-64::sip-6.7.12-py312h6a678d5_1 six pkgs/main/linux-64::six-1.17.0-py312h06a4308_0 sniffio pkgs/main/linux-64::sniffio-1.3.0-py312h06a4308_0 soupsieve pkgs/main/linux-64::soupsieve-2.5-py312h06a4308_0 stack_data pkgs/main/linux-64::stack_data-0.6.3-py312h06a4308_0 terminado pkgs/main/linux-64::terminado-0.17.1-py312h06a4308_0 tinycss2 pkgs/main/linux-64::tinycss2-1.4.0-py312h06a4308_0 tornado pkgs/main/linux-64::tornado-6.5.1-py312h5eee18b_0 traitlets pkgs/main/linux-64::traitlets-5.14.3-py312h06a4308_0 typing-extensions pkgs/main/linux-64::typing-extensions-4.15.0-py312h06a4308_0 typing_extensions pkgs/main/linux-64::typing_extensions-4.15.0-py312h06a4308_0 wcwidth pkgs/main/linux-64::wcwidth-0.2.13-py312h06a4308_0 webencodings pkgs/main/linux-64::webencodings-0.5.1-py312h06a4308_2 websocket-client pkgs/main/linux-64::websocket-client-1.8.0-py312h06a4308_0 widgetsnbextension pkgs/main/linux-64::widgetsnbextension-4.0.13-py312h06a4308_0 xcb-util pkgs/main/linux-64::xcb-util-0.4.1-h5eee18b_2 xcb-util-image pkgs/main/linux-64::xcb-util-image-0.4.0-h5eee18b_2 xcb-util-keysyms pkgs/main/linux-64::xcb-util-keysyms-0.4.1-h5eee18b_0 xcb-util-renderut~ pkgs/main/linux-64::xcb-util-renderutil-0.3.10-h5eee18b_0 xcb-util-wm pkgs/main/linux-64::xcb-util-wm-0.4.2-h5eee18b_0 xkeyboard-config pkgs/main/linux-64::xkeyboard-config-2.44-h5eee18b_0 xorg-libxdamage pkgs/main/linux-64::xorg-libxdamage-1.1.6-h9b100fa_0 xorg-libxfixes pkgs/main/linux-64::xorg-libxfixes-6.0.1-h9b100fa_0 xorg-libxshmfence pkgs/main/linux-64::xorg-libxshmfence-1.3.3-h9b100fa_0 xorg-libxxf86vm pkgs/main/linux-64::xorg-libxxf86vm-1.1.6-h9b100fa_0 yaml pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0 zeromq pkgs/main/linux-64::zeromq-4.3.5-h6a678d5_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done [ Info: Running nbconvert ... [NbConvertApp] WARNING | pattern '' matched no files [NbConvertApp] Converting notebook /home/pkgeval/.julia/packages/RCall/GLHIY/test/ijulia.ipynb to notebook Traceback (most recent call last): File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/jupyter_core/utils/__init__.py", line 154, in wrapped asyncio.get_running_loop() RuntimeError: no running event loop During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/pkgeval/.julia/conda/3/x86_64/bin/jupyter-nbconvert", line 11, in sys.exit(main()) ^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/jupyter_core/application.py", line 284, in launch_instance super().launch_instance(argv=argv, **kwargs) File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/traitlets/config/application.py", line 1075, in launch_instance app.start() File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 420, in start self.convert_notebooks() File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 597, in convert_notebooks self.convert_single_notebook(notebook_filename) File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 563, in convert_single_notebook output, resources = self.export_single_notebook( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 487, in export_single_notebook output, resources = self.exporter.from_filename( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 201, in from_filename return self.from_file(f, resources=resources, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 220, in from_file return self.from_notebook_node( ^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/nbconvert/exporters/notebook.py", line 36, in from_notebook_node nb_copy, resources = super().from_notebook_node(nb, resources, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 154, in from_notebook_node nb_copy, resources = self._preprocess(nb_copy, resources) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 353, in _preprocess nbc, resc = preprocessor(nbc, resc) ^^^^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/nbconvert/preprocessors/base.py", line 48, in __call__ return self.preprocess(nb, resources) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/nbconvert/preprocessors/execute.py", line 103, in preprocess self.preprocess_cell(cell, resources, index) File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/nbconvert/preprocessors/execute.py", line 124, in preprocess_cell cell = self.execute_cell(cell, index, store_history=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/jupyter_core/utils/__init__.py", line 158, in wrapped return loop.run_until_complete(inner) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/asyncio/base_events.py", line 691, in run_until_complete return future.result() ^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ using RCall RCall.ijulia_init() R"plot(1:10, 1:10)" ------------------ ----- stderr ----- [ Info: Precompiling RCall [6f49c342-dc21-5d91-9882-a32aef131414] (cache misses: mismatched flags (3)) ----- stderr ----- ERROR:  ----- stderr ----- LoadError: ----- stderr ----- ArgumentError: Package Preferences [21216c6a-2e73-6563-6e65-726566657250] is required but does not seem to be installed: - Run `Pkg.instantiate()` to install all recorded dependencies. Stacktrace: [1] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base ./loading.jl:2587 [2] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base ./loading.jl:2465 [3] macro expansion  @ ./loading.jl:2393 [inlined] [4] macro expansion  @ ./lock.jl:376 [inlined] [5] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2358 [6] require(into::Module, mod::Symbol)  @ Base ./loading.jl:2334 [7] top-level scope  @ ~/.julia/packages/RCall/GLHIY/src/RCall.jl:3 [8] include(mod::Module, _path::String)  @ Base ./Base.jl:305 [9] ----- stderr ----- include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:2997 [10] top-level scope  @ stdin:5 [11] eval(m::Module, e::Any)  @ Core ./boot.jl:489 [12] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:2843 [13] include_string  @ ./loading.jl:2853 [inlined] [14] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:319 [15] _start()  @ Base ./client.jl:554 in expression starting at /home/pkgeval/.julia/packages/RCall/GLHIY/src/RCall.jl:1 in expression starting at stdin:5 ------------------ Failed to precompile RCall [6f49c342-dc21-5d91-9882-a32aef131414] to "/home/pkgeval/.julia/compiled/v1.12/RCall/jl_Fqk96X". Stacktrace: [1] error(s::String)  @ Base ./error.jl:44 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)  @ Base ./loading.jl:3284 [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}})()  @ Base ./loading.jl:2652 [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})  @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:93 [5] #mkpidlock#7  @ /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:88 [inlined] [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})  @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:114 [7] #invokelatest_gr#232  @ ./reflection.jl:1282 [inlined] [8] invokelatest_gr  @ ./reflection.jl:1274 [inlined] [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)  @ Base ./loading.jl:3855 [10] maybe_cachefile_lock  @ ./loading.jl:3852 [inlined] [11] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base ./loading.jl:2638 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base ./loading.jl:2465 [13] macro expansion  @ ./loading.jl:2393 [inlined] [14] macro expansion  @ ./lock.jl:376 [inlined] [15] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2358 [16] require(into::Module, mod::Symbol)  @ Base ./loading.jl:2334 [17] eval(m::Module, e::Any)  @ Core ./boot.jl:489 ===================================================== IJulia: Error During Test at /home/pkgeval/.julia/packages/RCall/GLHIY/test/runtests.jl:80 Got exception outside of a @test LoadError: failed process: Process(`/home/pkgeval/.julia/conda/3/x86_64/bin/jupyter nbconvert --ExecutePreprocessor.timeout=-1 --to notebook --execute /home/pkgeval/.julia/packages/RCall/GLHIY/test/ijulia.ipynb '' --output /home/pkgeval/.julia/packages/RCall/GLHIY/test/ijulia.ipynb`, ProcessExited(1)) [1] Stacktrace: [1] pipeline_error @ ./process.jl:598 [inlined] [2] read(cmd::Cmd) @ Base ./process.jl:482 [3] read @ ./process.jl:491 [inlined] [4] notebook(source::String; out_path::String, timeout::Int64, nbconvert_options::String, jupyter_path::String) @ Weave ~/.julia/packages/Weave/f7Ly3/src/Weave.jl:296 [5] top-level scope @ ~/.julia/packages/RCall/GLHIY/test/ijulia.jl:14 [6] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [7] macro expansion @ ~/.julia/packages/RCall/GLHIY/test/runtests.jl:81 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [9] macro expansion @ ~/.julia/packages/RCall/GLHIY/test/runtests.jl:81 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [11] top-level scope @ ~/.julia/packages/RCall/GLHIY/test/runtests.jl:48 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [13] top-level scope @ none:6 [14] eval(m::Module, e::Any) @ Core ./boot.jl:489 [15] exec_options(opts::Base.JLOptions) @ Base ./client.jl:287 [16] _start() @ Base ./client.jl:554 in expression starting at /home/pkgeval/.julia/packages/RCall/GLHIY/test/ijulia.jl:14 ===================================================== ┌ Info: └ RCall.conda_provided_r = true . Test Summary: | Pass Error Total Time RCall | 479 4 483 3m55.0s basic | 64 64 22.6s convert/base | 192 192 15.8s convert/missing | 28 28 2.0s convert/datetime | 86 86 6.6s convert/dataframe | 11 11 6.7s convert/categorical | 22 22 3.6s convert/formula | 16 16 10.4s convert/namedtuple | 10 10 1.9s convert/tuple | 11 11 0.4s macros | 17 17 1.1s namespaces | 1 1 4.0s repl | 20 2 22 25.4s IJulia | 1 1 2m13.8s ERROR: LoadError: Some tests did not pass: 479 passed, 0 failed, 4 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/RCall/GLHIY/test/runtests.jl:45 Testing failed after 241.28s ERROR: LoadError: Package RCall errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2427 [3] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2280 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:483 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:164 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 [7] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:151 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [10] include(mod::Module, _path::String) @ Base ./Base.jl:305 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:321 [12] _start() @ Base ./client.jl:554 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 440.3s: package fails to precompile