Package evaluation to test RCall on Julia 1.14.0-DEV.30 (073666df8b*) started at 2025-11-04T19:38:41.860 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.55s ################################################################################ # Installation # Installing RCall... Resolving package versions... Installed Conda ─ v1.10.3 Installed RCall ─ v0.14.9 Updating `~/.julia/environments/v1.14/Project.toml` [6f49c342] + RCall v0.14.9 Updating `~/.julia/environments/v1.14/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [324d7699] + CategoricalArrays v1.0.2 [34da2185] + Compat v4.18.1 [8f4d0f93] + Conda v1.10.3 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 ⌅ [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 v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [682c06a0] + JSON v1.2.0 [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 v3.1.0 [43287f4e] + PtrArrays v1.3.0 [6f49c342] + RCall v0.14.9 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [91c51154] + SentinelArrays v1.4.8 [1277b4bf] + ShiftedArrays v2.0.0 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.7 [4c63d2b9] + StatsFuns v1.5.2 [3eaba693] + StatsModels v0.7.7 [892a3eda] + StringManipulation v0.4.1 [ec057cc2] + StructUtils v2.5.1 [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 v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [b27032c2] + LibCURL v1.0.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown 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 v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [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 v8.16.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.9.9 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.67.1+0 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/8f06b0cfa4c514c7b9546756dbae91fcfbc92dc9/build.log` Building RCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/7521292e0ca900751cf0f35f2a2faf1cb321e960/build.log` Installation completed after 83.44s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ UndefVarError: `project_rel_path` not defined in `TestEnv` │ Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value. │ Stacktrace: │ [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:9 │ [6] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:24 │ [7] include(mod::Module, _path::String) │ @ Base ./Base.jl:309 │ [8] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:344 │ [9] _start() │ @ Base ./client.jl:577 └ @ Main /PkgEval.jl/scripts/precompile.jl:26 Precompiling package dependencies... Precompiling packages... 1140.4 ms ✓ WinReg 2221.1 ms ✓ CategoricalArrays → CategoricalArraysStatsBaseExt 2 dependencies successfully precompiled in 4 seconds. 80 already precompiled. Precompilation completed after 15.36s ################################################################################ # Testing # Testing RCall Test Could not use exact versions of packages in manifest, re-resolving. Note: if you do not check your manifest file into source control, then you can probably ignore this message. However, if you do check your manifest file into source control, then you probably want to pass the `allow_reresolve = false` kwarg when calling the `Pkg.test` function. Installed IJulia ─ v1.31.1 Updating `/tmp/jl_PPzh1Q/Project.toml` [39de3d68] + AxisArrays v0.4.8 [992eb4ea] + CondaPkg v0.2.33 [7073ff75] + IJulia v1.31.1 [6f49c342] + RCall v0.14.9 [98d24dd4] + TestSetExtensions v3.0.0 [44d3d7a6] + Weave v0.10.12 [44cfe95a] ~ Pkg ⇒ v1.13.0 [8dfed614] ~ Test ⇒ v1.11.0 Updating `/tmp/jl_PPzh1Q/Manifest.toml` [39de3d68] + AxisArrays v0.4.8 [992eb4ea] + CondaPkg v0.2.33 [ab62b9b5] + DeepDiffs v1.2.0 [eafb193a] + Highlights v0.5.3 [7073ff75] + IJulia v1.31.1 [8197267c] + IntervalSets v0.7.11 [c8e1da08] + IterTools v1.10.0 ⌅ [682c06a0] ↓ JSON v1.2.0 ⇒ v0.21.4 [0f8b85d8] + JSON3 v1.14.3 [0b3b1443] + MicroMamba v0.1.14 [ffc61752] + Mustache v1.0.21 [fa939f87] + Pidfile v1.3.0 [6f49c342] + RCall v0.14.9 [b3c3ace0] + RangeArrays v0.3.2 [05181044] + RelocatableFolders v1.0.1 [6c6a2e73] + Scratch v1.3.0 [69024149] + StringEncodings v0.3.7 [856f2bd8] + StructTypes v1.11.0 [ec057cc2] - StructUtils v2.5.1 [98d24dd4] + TestSetExtensions v3.0.0 [44d3d7a6] + Weave v0.10.12 [ddb6d928] + YAML v0.4.14 [c2297ded] + ZMQ v1.5.0 [94ce4f54] + Libiconv_jll v1.18.0+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 [8ba89e20] + Distributed v1.11.0 [4af54fe1] + LazyArtifacts v1.11.0 [76f85450] + LibGit2 v1.11.0 [a63ad114] + Mmap v1.11.0 [44cfe95a] ~ Pkg ⇒ v1.13.0 [a4e569a6] + Tar v1.10.0 [8dfed614] ~ Test ⇒ v1.11.0 [e37daf67] + LibGit2_jll v1.9.1+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [3f19e933] + p7zip_jll v17.6.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Building IJulia → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/cdda5c1e16dace665ea5481460a3b6728f24a825/build.log` Test Successfully re-resolved Status `/tmp/jl_PPzh1Q/Project.toml` [39de3d68] AxisArrays v0.4.8 [324d7699] CategoricalArrays v1.0.2 [8f4d0f93] Conda v1.10.3 [992eb4ea] CondaPkg v0.2.33 [a93c6f00] DataFrames v1.8.1 ⌅ [864edb3b] DataStructures v0.18.22 [7073ff75] IJulia v1.31.1 [21216c6a] Preferences v1.5.0 [6f49c342] RCall v0.14.9 [3eaba693] StatsModels v0.7.7 [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 v1.13.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_PPzh1Q/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [39de3d68] AxisArrays v0.4.8 [324d7699] CategoricalArrays v1.0.2 [34da2185] Compat v4.18.1 [8f4d0f93] Conda v1.10.3 [992eb4ea] CondaPkg v0.2.33 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 ⌅ [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 v1.31.1 [842dd82b] InlineStrings v1.4.5 [8197267c] IntervalSets v0.7.11 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [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 v3.1.0 [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 v0.9.0 [6c6a2e73] Scratch v1.3.0 [91c51154] SentinelArrays v1.4.8 [1277b4bf] ShiftedArrays v2.0.0 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.7 [4c63d2b9] StatsFuns v1.5.2 [3eaba693] StatsModels v0.7.7 [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 v1.5.0 [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 v1.7.0 [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 v1.0.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.13.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [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 v8.16.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.9.9 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.67.1+0 [3f19e933] p7zip_jll v17.6.0+0 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 7.6s ┌ 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 4.5.2 (2025-10-31) 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-r0.3.30.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_4.5.2 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:310 [9] top-level scope @ ~/.julia/packages/RCall/GLHIY/test/runtests.jl:72 [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [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/v1.14/Test/src/Test.jl:1961 [inlined] [15] top-level scope @ ~/.julia/packages/RCall/GLHIY/test/runtests.jl:48 [16] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [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:310 [20] _start() @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/RCall/GLHIY/test/namespaces.jl:5 ===================================================== ===================================================== repl: Error During Test at /home/pkgeval/.julia/packages/RCall/GLHIY/test/runtests.jl:71 Got exception outside of a @test LoadError: UndefRefError: access to undefined reference Stacktrace: [1] getproperty @ ./Base_compiler.jl:57 [inlined] [2] repl_init(repl::LineEditREPL) @ RCall.RPrompt ~/.julia/packages/RCall/GLHIY/src/RPrompt.jl:228 [3] top-level scope @ ~/.julia/packages/RCall/GLHIY/test/repl.jl:53 [4] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [5] top-level scope @ ~/.julia/packages/RCall/GLHIY/test/runtests.jl:72 [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [7] macro expansion @ ~/.julia/packages/RCall/GLHIY/test/runtests.jl:72 [inlined] [8] eval(m::Module, e::Any) @ Core ./boot.jl:489 [9] macro expansion @ ~/.julia/packages/RCall/GLHIY/test/runtests.jl:71 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [11] top-level scope @ ~/.julia/packages/RCall/GLHIY/test/runtests.jl:48 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [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:310 [16] _start() @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/RCall/GLHIY/test/repl.jl:53 ===================================================== [ Info: Installing 'julia 1.14.0-DEV' kernelspec in /home/pkgeval/.local/share/jupyter/kernels/julia-1.14 [ Info: Running `conda install -q -y jupyter` in root environment Channels: - r - 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 ---------------------------|----------------- _python_abi3_support-1.0 | hd8ed1ab_2 8 KB conda-forge anyio-4.11.0 | pyhcf101f3_0 135 KB conda-forge argon2-cffi-25.1.0 | pyhd8ed1ab_0 18 KB conda-forge argon2-cffi-bindings-25.1.0| py312h4c3975b_1 35 KB conda-forge arrow-1.4.0 | pyhcf101f3_0 111 KB conda-forge asttokens-3.0.0 | pyhd8ed1ab_1 28 KB conda-forge async-lru-2.0.5 | pyh29332c3_0 17 KB conda-forge attrs-25.4.0 | pyh71513ae_0 59 KB conda-forge babel-2.17.0 | pyhd8ed1ab_0 6.6 MB conda-forge beautifulsoup4-4.14.2 | pyha770c72_0 87 KB conda-forge bleach-6.2.0 | pyh29332c3_4 138 KB conda-forge bleach-with-css-6.2.0 | h82add2a_4 4 KB conda-forge cached-property-1.5.2 | hd8ed1ab_1 4 KB conda-forge cached_property-1.5.2 | pyha770c72_1 11 KB conda-forge comm-0.2.3 | pyhe01879c_0 14 KB conda-forge cpython-3.12.12 | py312hd8ed1ab_1 45 KB conda-forge debugpy-1.8.17 | py312h8285ef7_0 2.7 MB conda-forge decorator-5.2.1 | pyhd8ed1ab_0 14 KB conda-forge defusedxml-0.7.1 | pyhd8ed1ab_0 23 KB conda-forge exceptiongroup-1.3.0 | pyhd8ed1ab_0 21 KB conda-forge executing-2.2.1 | pyhd8ed1ab_0 30 KB conda-forge fqdn-1.5.1 | pyhd8ed1ab_1 16 KB conda-forge h11-0.16.0 | pyhd8ed1ab_0 37 KB conda-forge httpcore-1.0.9 | pyh29332c3_0 48 KB conda-forge httpx-0.28.1 | pyhd8ed1ab_0 62 KB conda-forge importlib-metadata-8.7.0 | pyhe01879c_1 34 KB conda-forge ipykernel-7.1.0 | pyha191276_0 131 KB conda-forge ipython-9.6.0 | pyhfa0c392_0 624 KB conda-forge ipython_pygments_lexers-1.1.1| pyhd8ed1ab_0 14 KB conda-forge ipywidgets-8.1.8 | pyhd8ed1ab_0 112 KB conda-forge isoduration-20.11.0 | pyhd8ed1ab_1 19 KB conda-forge jedi-0.19.2 | pyhd8ed1ab_1 824 KB conda-forge jinja2-3.1.6 | pyhd8ed1ab_0 110 KB conda-forge json5-0.12.1 | pyhd8ed1ab_0 33 KB conda-forge jsonschema-4.25.1 | pyhe01879c_0 80 KB conda-forge jsonschema-specifications-2025.9.1| pyhcf101f3_0 19 KB conda-forge jsonschema-with-format-nongpl-4.25.1| he01879c_0 5 KB conda-forge jupyter-1.1.1 | pyhd8ed1ab_1 9 KB conda-forge jupyter-lsp-2.3.0 | pyhcf101f3_0 59 KB conda-forge jupyter_client-8.6.3 | pyhd8ed1ab_1 104 KB conda-forge jupyter_console-6.6.3 | pyhd8ed1ab_1 26 KB conda-forge jupyter_core-5.9.1 | pyhc90fa1f_0 64 KB conda-forge jupyter_events-0.12.0 | pyh29332c3_0 23 KB conda-forge jupyter_server-2.17.0 | pyhcf101f3_0 339 KB conda-forge jupyter_server_terminals-0.5.3| pyhd8ed1ab_1 19 KB conda-forge jupyterlab-4.4.10 | pyhd8ed1ab_0 7.7 MB conda-forge jupyterlab_pygments-0.3.0 | pyhd8ed1ab_2 18 KB conda-forge jupyterlab_server-2.28.0 | pyhcf101f3_0 50 KB conda-forge jupyterlab_widgets-3.0.16 | pyhcf101f3_1 212 KB conda-forge lark-1.3.1 | pyhd8ed1ab_0 92 KB conda-forge libsodium-1.0.20 | h4ab18f5_0 201 KB conda-forge markupsafe-3.0.3 | py312h8a5da7c_0 25 KB conda-forge matplotlib-inline-0.2.1 | pyhd8ed1ab_0 15 KB conda-forge mistune-3.1.4 | pyhcf101f3_0 71 KB conda-forge nbclient-0.10.2 | pyhd8ed1ab_0 27 KB conda-forge nbconvert-core-7.16.6 | pyhcf101f3_1 195 KB conda-forge nbformat-5.10.4 | pyhd8ed1ab_1 99 KB conda-forge nest-asyncio-1.6.0 | pyhd8ed1ab_1 11 KB conda-forge notebook-7.4.7 | pyhd8ed1ab_0 9.9 MB conda-forge notebook-shim-0.2.4 | pyhd8ed1ab_1 16 KB conda-forge overrides-7.7.0 | pyhd8ed1ab_1 29 KB conda-forge pandocfilters-1.5.0 | pyhd8ed1ab_0 11 KB conda-forge parso-0.8.5 | pyhcf101f3_0 80 KB conda-forge pexpect-4.9.0 | pyhd8ed1ab_1 52 KB conda-forge pickleshare-0.7.5 | pyhd8ed1ab_1004 11 KB conda-forge prometheus_client-0.23.1 | pyhd8ed1ab_0 53 KB conda-forge prompt-toolkit-3.0.52 | pyha770c72_0 268 KB conda-forge prompt_toolkit-3.0.52 | hd8ed1ab_0 7 KB conda-forge psutil-7.1.3 | py312h5253ce2_0 483 KB conda-forge ptyprocess-0.7.0 | pyhd8ed1ab_1 19 KB conda-forge pure_eval-0.2.3 | pyhd8ed1ab_1 16 KB conda-forge pygments-2.19.2 | pyhd8ed1ab_0 868 KB conda-forge python-dateutil-2.9.0.post0| pyhe01879c_2 228 KB conda-forge python-fastjsonschema-2.21.2| pyhe01879c_0 239 KB conda-forge python-gil-3.12.12 | hd8ed1ab_1 45 KB conda-forge python-json-logger-2.0.7 | pyhd8ed1ab_0 13 KB conda-forge python-tzdata-2025.2 | pyhd8ed1ab_0 141 KB conda-forge pytz-2025.2 | pyhd8ed1ab_0 185 KB conda-forge pyyaml-6.0.3 | py312h8a5da7c_0 200 KB conda-forge pyzmq-27.1.0 | py312hfb55c3c_0 207 KB conda-forge referencing-0.37.0 | pyhcf101f3_0 51 KB conda-forge rfc3339-validator-0.1.4 | pyhd8ed1ab_1 10 KB conda-forge rfc3986-validator-0.1.1 | pyh9f0ad1d_0 8 KB conda-forge rfc3987-syntax-1.1.0 | pyhe01879c_1 22 KB conda-forge rpds-py-0.28.0 | py312h868fb18_1 372 KB conda-forge send2trash-1.8.3 | pyh0d859eb_1 22 KB conda-forge six-1.17.0 | pyhe01879c_1 18 KB conda-forge sniffio-1.3.1 | pyhd8ed1ab_1 15 KB conda-forge soupsieve-2.8 | pyhd8ed1ab_0 37 KB conda-forge stack_data-0.6.3 | pyhd8ed1ab_1 26 KB conda-forge terminado-0.18.1 | pyh0d859eb_0 22 KB conda-forge tinycss2-1.4.0 | pyhd8ed1ab_0 28 KB conda-forge tomli-2.3.0 | pyhcf101f3_0 20 KB conda-forge tornado-6.5.2 | py312h4c3975b_1 831 KB conda-forge traitlets-5.14.3 | pyhd8ed1ab_1 107 KB conda-forge typing-extensions-4.15.0 | h396c80c_0 89 KB conda-forge typing_extensions-4.15.0 | pyhcf101f3_0 50 KB conda-forge typing_utils-0.1.0 | pyhd8ed1ab_1 15 KB conda-forge uri-template-1.3.0 | pyhd8ed1ab_1 23 KB conda-forge wcwidth-0.2.14 | pyhd8ed1ab_0 33 KB conda-forge webcolors-25.10.0 | pyhd8ed1ab_0 19 KB conda-forge webencodings-0.5.1 | pyhd8ed1ab_3 15 KB conda-forge websocket-client-1.9.0 | pyhd8ed1ab_0 60 KB conda-forge widgetsnbextension-4.0.15 | pyhd8ed1ab_0 868 KB conda-forge yaml-0.2.5 | h280c20c_3 83 KB conda-forge zeromq-4.3.5 | h387f397_9 303 KB conda-forge zipp-3.23.0 | pyhd8ed1ab_0 22 KB conda-forge ------------------------------------------------------------ Total: 37.6 MB The following NEW packages will be INSTALLED: _python_abi3_supp~ conda-forge/noarch::_python_abi3_support-1.0-hd8ed1ab_2 anyio conda-forge/noarch::anyio-4.11.0-pyhcf101f3_0 argon2-cffi conda-forge/noarch::argon2-cffi-25.1.0-pyhd8ed1ab_0 argon2-cffi-bindi~ conda-forge/linux-64::argon2-cffi-bindings-25.1.0-py312h4c3975b_1 arrow conda-forge/noarch::arrow-1.4.0-pyhcf101f3_0 asttokens conda-forge/noarch::asttokens-3.0.0-pyhd8ed1ab_1 async-lru conda-forge/noarch::async-lru-2.0.5-pyh29332c3_0 attrs conda-forge/noarch::attrs-25.4.0-pyh71513ae_0 babel conda-forge/noarch::babel-2.17.0-pyhd8ed1ab_0 beautifulsoup4 conda-forge/noarch::beautifulsoup4-4.14.2-pyha770c72_0 bleach conda-forge/noarch::bleach-6.2.0-pyh29332c3_4 bleach-with-css conda-forge/noarch::bleach-with-css-6.2.0-h82add2a_4 cached-property conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1 cached_property conda-forge/noarch::cached_property-1.5.2-pyha770c72_1 comm conda-forge/noarch::comm-0.2.3-pyhe01879c_0 cpython conda-forge/noarch::cpython-3.12.12-py312hd8ed1ab_1 debugpy conda-forge/linux-64::debugpy-1.8.17-py312h8285ef7_0 decorator conda-forge/noarch::decorator-5.2.1-pyhd8ed1ab_0 defusedxml conda-forge/noarch::defusedxml-0.7.1-pyhd8ed1ab_0 exceptiongroup conda-forge/noarch::exceptiongroup-1.3.0-pyhd8ed1ab_0 executing conda-forge/noarch::executing-2.2.1-pyhd8ed1ab_0 fqdn conda-forge/noarch::fqdn-1.5.1-pyhd8ed1ab_1 h11 conda-forge/noarch::h11-0.16.0-pyhd8ed1ab_0 httpcore conda-forge/noarch::httpcore-1.0.9-pyh29332c3_0 httpx conda-forge/noarch::httpx-0.28.1-pyhd8ed1ab_0 importlib-metadata conda-forge/noarch::importlib-metadata-8.7.0-pyhe01879c_1 ipykernel conda-forge/noarch::ipykernel-7.1.0-pyha191276_0 ipython conda-forge/noarch::ipython-9.6.0-pyhfa0c392_0 ipython_pygments_~ conda-forge/noarch::ipython_pygments_lexers-1.1.1-pyhd8ed1ab_0 ipywidgets conda-forge/noarch::ipywidgets-8.1.8-pyhd8ed1ab_0 isoduration conda-forge/noarch::isoduration-20.11.0-pyhd8ed1ab_1 jedi conda-forge/noarch::jedi-0.19.2-pyhd8ed1ab_1 jinja2 conda-forge/noarch::jinja2-3.1.6-pyhd8ed1ab_0 json5 conda-forge/noarch::json5-0.12.1-pyhd8ed1ab_0 jsonschema conda-forge/noarch::jsonschema-4.25.1-pyhe01879c_0 jsonschema-specif~ conda-forge/noarch::jsonschema-specifications-2025.9.1-pyhcf101f3_0 jsonschema-with-f~ conda-forge/noarch::jsonschema-with-format-nongpl-4.25.1-he01879c_0 jupyter conda-forge/noarch::jupyter-1.1.1-pyhd8ed1ab_1 jupyter-lsp conda-forge/noarch::jupyter-lsp-2.3.0-pyhcf101f3_0 jupyter_client conda-forge/noarch::jupyter_client-8.6.3-pyhd8ed1ab_1 jupyter_console conda-forge/noarch::jupyter_console-6.6.3-pyhd8ed1ab_1 jupyter_core conda-forge/noarch::jupyter_core-5.9.1-pyhc90fa1f_0 jupyter_events conda-forge/noarch::jupyter_events-0.12.0-pyh29332c3_0 jupyter_server conda-forge/noarch::jupyter_server-2.17.0-pyhcf101f3_0 jupyter_server_te~ conda-forge/noarch::jupyter_server_terminals-0.5.3-pyhd8ed1ab_1 jupyterlab conda-forge/noarch::jupyterlab-4.4.10-pyhd8ed1ab_0 jupyterlab_pygmen~ conda-forge/noarch::jupyterlab_pygments-0.3.0-pyhd8ed1ab_2 jupyterlab_server conda-forge/noarch::jupyterlab_server-2.28.0-pyhcf101f3_0 jupyterlab_widgets conda-forge/noarch::jupyterlab_widgets-3.0.16-pyhcf101f3_1 lark conda-forge/noarch::lark-1.3.1-pyhd8ed1ab_0 libsodium conda-forge/linux-64::libsodium-1.0.20-h4ab18f5_0 markupsafe conda-forge/linux-64::markupsafe-3.0.3-py312h8a5da7c_0 matplotlib-inline conda-forge/noarch::matplotlib-inline-0.2.1-pyhd8ed1ab_0 mistune conda-forge/noarch::mistune-3.1.4-pyhcf101f3_0 nbclient conda-forge/noarch::nbclient-0.10.2-pyhd8ed1ab_0 nbconvert-core conda-forge/noarch::nbconvert-core-7.16.6-pyhcf101f3_1 nbformat conda-forge/noarch::nbformat-5.10.4-pyhd8ed1ab_1 nest-asyncio conda-forge/noarch::nest-asyncio-1.6.0-pyhd8ed1ab_1 notebook conda-forge/noarch::notebook-7.4.7-pyhd8ed1ab_0 notebook-shim conda-forge/noarch::notebook-shim-0.2.4-pyhd8ed1ab_1 overrides conda-forge/noarch::overrides-7.7.0-pyhd8ed1ab_1 pandocfilters conda-forge/noarch::pandocfilters-1.5.0-pyhd8ed1ab_0 parso conda-forge/noarch::parso-0.8.5-pyhcf101f3_0 pexpect conda-forge/noarch::pexpect-4.9.0-pyhd8ed1ab_1 pickleshare conda-forge/noarch::pickleshare-0.7.5-pyhd8ed1ab_1004 prometheus_client conda-forge/noarch::prometheus_client-0.23.1-pyhd8ed1ab_0 prompt-toolkit conda-forge/noarch::prompt-toolkit-3.0.52-pyha770c72_0 prompt_toolkit conda-forge/noarch::prompt_toolkit-3.0.52-hd8ed1ab_0 psutil conda-forge/linux-64::psutil-7.1.3-py312h5253ce2_0 ptyprocess conda-forge/noarch::ptyprocess-0.7.0-pyhd8ed1ab_1 pure_eval conda-forge/noarch::pure_eval-0.2.3-pyhd8ed1ab_1 pygments conda-forge/noarch::pygments-2.19.2-pyhd8ed1ab_0 python-dateutil conda-forge/noarch::python-dateutil-2.9.0.post0-pyhe01879c_2 python-fastjsonsc~ conda-forge/noarch::python-fastjsonschema-2.21.2-pyhe01879c_0 python-gil conda-forge/noarch::python-gil-3.12.12-hd8ed1ab_1 python-json-logger conda-forge/noarch::python-json-logger-2.0.7-pyhd8ed1ab_0 python-tzdata conda-forge/noarch::python-tzdata-2025.2-pyhd8ed1ab_0 pytz conda-forge/noarch::pytz-2025.2-pyhd8ed1ab_0 pyyaml conda-forge/linux-64::pyyaml-6.0.3-py312h8a5da7c_0 pyzmq conda-forge/linux-64::pyzmq-27.1.0-py312hfb55c3c_0 referencing conda-forge/noarch::referencing-0.37.0-pyhcf101f3_0 rfc3339-validator conda-forge/noarch::rfc3339-validator-0.1.4-pyhd8ed1ab_1 rfc3986-validator conda-forge/noarch::rfc3986-validator-0.1.1-pyh9f0ad1d_0 rfc3987-syntax conda-forge/noarch::rfc3987-syntax-1.1.0-pyhe01879c_1 rpds-py conda-forge/linux-64::rpds-py-0.28.0-py312h868fb18_1 send2trash conda-forge/noarch::send2trash-1.8.3-pyh0d859eb_1 six conda-forge/noarch::six-1.17.0-pyhe01879c_1 sniffio conda-forge/noarch::sniffio-1.3.1-pyhd8ed1ab_1 soupsieve conda-forge/noarch::soupsieve-2.8-pyhd8ed1ab_0 stack_data conda-forge/noarch::stack_data-0.6.3-pyhd8ed1ab_1 terminado conda-forge/noarch::terminado-0.18.1-pyh0d859eb_0 tinycss2 conda-forge/noarch::tinycss2-1.4.0-pyhd8ed1ab_0 tomli conda-forge/noarch::tomli-2.3.0-pyhcf101f3_0 tornado conda-forge/linux-64::tornado-6.5.2-py312h4c3975b_1 traitlets conda-forge/noarch::traitlets-5.14.3-pyhd8ed1ab_1 typing-extensions conda-forge/noarch::typing-extensions-4.15.0-h396c80c_0 typing_extensions conda-forge/noarch::typing_extensions-4.15.0-pyhcf101f3_0 typing_utils conda-forge/noarch::typing_utils-0.1.0-pyhd8ed1ab_1 uri-template conda-forge/noarch::uri-template-1.3.0-pyhd8ed1ab_1 wcwidth conda-forge/noarch::wcwidth-0.2.14-pyhd8ed1ab_0 webcolors conda-forge/noarch::webcolors-25.10.0-pyhd8ed1ab_0 webencodings conda-forge/noarch::webencodings-0.5.1-pyhd8ed1ab_3 websocket-client conda-forge/noarch::websocket-client-1.9.0-pyhd8ed1ab_0 widgetsnbextension conda-forge/noarch::widgetsnbextension-4.0.15-pyhd8ed1ab_0 yaml conda-forge/linux-64::yaml-0.2.5-h280c20c_3 zeromq conda-forge/linux-64::zeromq-4.3.5-h387f397_9 zipp conda-forge/noarch::zipp-3.23.0-pyhd8ed1ab_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 [ Info: Precompiling IJulia [7073ff75-c697-5162-941a-fcdaad2a7d2a] (caches not reused: 1 for dependency source file not found, 2 for different compilation options) Precompiling packages... 51470.7 ms ✓ IJulia (serial) 1 dependency successfully precompiled in 52 seconds Traceback (most recent call last): File "/home/pkgeval/.julia/conda/3/x86_64/bin/jupyter-nbconvert", line 10, 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 165, 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] ----- stderr ----- ┌ Info: Skipping precompilation due to precompilable error. Importing RCall [6f49c342-dc21-5d91-9882-a32aef131414]. └  exception = Error when precompiling module, potentially caused by a __precompile__(false) declaration in the module. ------------------ LoadError: ArgumentError: Package CategoricalArrays [324d7699-5711-5eae-9e2f-1d82baa6b597] is required but does not seem to be installed: - Run `Pkg.instantiate()` to install all recorded dependencies. in expression starting at /home/pkgeval/.julia/packages/RCall/GLHIY/src/RCall.jl:1 Stacktrace: [1] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base ./loading.jl:2698 [2] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base ./loading.jl:2576 [3] macro expansion  @ ./loading.jl:2504 [inlined] [4] macro expansion  @ ./lock.jl:376 [inlined] [5] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2468 [6] require  @ ./loading.jl:2444 [inlined] [7] eval_import_path  @ ./module.jl:36 [inlined] [8] eval_import_path_all(at::Module, path::Expr, keyword::String)  @ Base ./module.jl:60 [9] _eval_using  @ ./module.jl:137 [inlined] [10] _eval_using(to::Module, path::Expr)  @ Base ./module.jl:137 [11] top-level scope  @ ~/.julia/packages/RCall/GLHIY/src/RCall.jl:8 [12] include(mod::Module, _path::String)  @ Base ./Base.jl:309 [13] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base ./loading.jl:2817 [14] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base ./loading.jl:2576 [15] macro expansion  @ ./loading.jl:2504 [inlined] [16] macro expansion  @ ./lock.jl:376 [inlined] [17] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2468 [18] require  @ ./loading.jl:2444 [inlined] [19] eval_import_path  @ ./module.jl:36 [inlined] [20] eval_import_path_all(at::Module, path::Expr, keyword::String)  @ Base ./module.jl:60 [21] _eval_using  @ ./module.jl:137 [inlined] [22] _eval_using(to::Module, path::Expr)  @ Base ./module.jl:137 [23] top-level scope  @ In[1]:1 [24] 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:611 [inlined] [2] read(cmd::Cmd) @ Base ./process.jl:491 [3] read @ ./process.jl:500 [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] kwcall(::@NamedTuple{out_path::String, jupyter_path::String}, ::typeof(Weave.notebook), source::String) @ Weave ~/.julia/packages/Weave/f7Ly3/src/Weave.jl:281 [6] top-level scope @ ~/.julia/packages/RCall/GLHIY/test/ijulia.jl:14 [7] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [8] macro expansion @ ~/.julia/packages/RCall/GLHIY/test/runtests.jl:81 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [10] macro expansion @ ~/.julia/packages/RCall/GLHIY/test/runtests.jl:81 [inlined] [11] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [12] top-level scope @ ~/.julia/packages/RCall/GLHIY/test/runtests.jl:48 [13] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [14] top-level scope @ none:6 [15] eval(m::Module, e::Any) @ Core ./boot.jl:489 [16] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [17] _start() @ Base ./client.jl:577 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 | 459 3 462 3m57.1s basic | 64 64 19.4s convert/base | 192 192 14.1s convert/missing | 28 28 1.9s convert/datetime | 86 86 5.0s convert/dataframe | 11 11 3.9s convert/categorical | 22 22 3.4s convert/formula | 16 16 9.0s convert/namedtuple | 10 10 1.7s convert/tuple | 11 11 0.4s macros | 17 17 1.1s namespaces | 1 1 3.7s repl | 1 1 35.3s IJulia | 1 1 2m17.7s ERROR: LoadError: Some tests did not pass: 459 passed, 0 failed, 3 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/RCall/GLHIY/test/runtests.jl:45 Testing failed after 277.88s ERROR: LoadError: Package RCall errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2946 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2795 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:572 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:548 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 451.11s: package tests unexpectedly errored