CRAN Package Check Results for Package jlmerclusterperm

Last updated on 2024-02-26 08:48:48 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1.2 3.21 45.98 49.19 OK
r-devel-linux-x86_64-debian-gcc 1.1.2 3.09 35.53 38.62 OK
r-devel-linux-x86_64-fedora-clang 1.1.2 62.67 OK
r-devel-linux-x86_64-fedora-gcc 1.1.2 40.92 OK
r-devel-windows-x86_64 1.1.2 5.00 315.00 320.00 OK
r-patched-linux-x86_64 1.1.2 3.93 43.10 47.03 OK
r-release-linux-x86_64 1.1.2 2.64 42.82 45.46 OK
r-release-macos-arm64 1.1.2 34.00 OK
r-release-macos-x86_64 1.1.2 70.00 OK
r-release-windows-x86_64 1.1.2 6.00 337.00 343.00 ERROR
r-oldrel-macos-arm64 1.1.2 30.00 OK
r-oldrel-windows-x86_64 1.1.2 6.00 334.00 340.00 ERROR

Additional issues

donttest

Check Details

Version: 1.1.2
Check: tests
Result: ERROR Running 'testthat.R' [269s] Running the tests in 'tests/testthat.R' failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(jlmerclusterperm) > > test_check("jlmerclusterperm") Julia Version 1.8.0 Commit 5544a0fab7 (2022-08-17 13:38 UTC) Platform Info: OS: Windows (x86_64-w64-mingw32) CPU: 56 × Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-13.0.1 (ORCJIT, broadwell) Threads: 1 on 56 virtual cores nothing ℹ Starting Julia with 2 threads ✔ Starting Julia with 2 threads [7.4s] ℹ Activating package environment ✔ Activating package environment [16.5s] Status `C:\Users\CRAN\AppData\Local\R\cache\R\jlmerclusterperm\julia\Project.toml` [a93c6f00] DataFrames v1.6.1 [31c24e10] Distributions v0.25.103 [38e38edf] GLM v1.9.0 [2a59065a] JlmerClusterPerm v0.1.1 `JlmerClusterPerm` [ff71e718] MixedModels v4.22.2 [92933f4c] ProgressMeter v1.9.0 [74087812] Random123 v1.6.1 ⌃ [2913bbd2] StatsBase v0.33.21 [3eaba693] StatsModels v0.7.3 [fd094767] Suppressor v0.2.6 [9a3f8284] Random Info Packages marked with ⌃ have new versions available # This file is machine-generated - editing it directly is not advised julia_version = "1.8.0" manifest_format = "2.0" project_hash = "998a3e62f1f1411e2e150f96d1c48126701e35d7" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] git-tree-sha1 = "02f731463748db57cc2ebfbd9fbc9ce8280d3433" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" version = "3.7.1" [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" version = "1.1.1" [[deps.ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra", "SparseArrays"] git-tree-sha1 = "af43df5704827c8618afd36eb56fcab20d3041ee" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" version = "1.4.3" [[deps.Arrow]] deps = 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"PrecompileTools", "SparseArrays"] git-tree-sha1 = "06a2a94d5a4979c36cc7a3c28d70800f448ae5bb" uuid = "aae01518-5342-5314-be14-df237901396f" version = "1.3.0" [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" [[deps.BenchmarkTools]] deps = ["JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"] git-tree-sha1 = "f1f03a9fa24271160ed7e73051fba3c1a759b53f" uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" version = "1.4.0" [[deps.BitIntegers]] deps = ["Random"] git-tree-sha1 = "a55462dfddabc34bc97d3a7403a2ca2802179ae6" uuid = "c3b6d118-76ef-56ca-8cc7-ebb389d030a1" version = "0.3.1" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" version = "1.0.8+0" [[deps.CEnum]] git-tree-sha1 = "eb4cb44a499229b3b8426dcfb5dd85333951ff90" uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" version = "0.4.2" [[deps.Calculus]] deps = ["LinearAlgebra"] git-tree-sha1 = 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[[deps.Crayons]] git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15" uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" version = "4.1.1" [[deps.DataAPI]] git-tree-sha1 = "8da84edb865b0b5b0100c0666a9bc9a0b71c553c" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" version = "1.15.0" [[deps.DataFrames]] deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] git-tree-sha1 = "04c738083f29f86e62c8afc341f0967d8717bdb8" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" version = "1.6.1" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] git-tree-sha1 = "3dbd312d370723b6bb43ba9d02fc36abade4518d" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" version = "0.18.15" 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"7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] git-tree-sha1 = "31e996f0a15c7b280ba9f76636b3ff9e2ae58c9a" uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" version = "0.21.4" [[deps.JSON3]] deps = ["Dates", "Mmap", "Parsers", "PrecompileTools", "StructTypes", "UUIDs"] git-tree-sha1 = "95220473901735a0f4df9d1ca5b171b568b2daa3" uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" version = "1.13.2" [[deps.JlmerClusterPerm]] deps = ["DataFrames", "Distributions", "GLM", "MixedModels", "ProgressMeter", "Random", "Random123", "StatsBase", "StatsModels", "Suppressor"] path = "JlmerClusterPerm" uuid = "2a59065a-9564-4903-82dd-0e42ce19d0e1" version = "0.1.1" [[deps.LaTeXStrings]] git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" version = "1.3.1" [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] uuid = 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["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.TimeZones]] deps = ["Artifacts", "Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "RecipesBase", "Scratch", "TZJData", "Unicode", "p7zip_jll"] git-tree-sha1 = "89e64d61ef3cd9e80f7fc12b7d13db2d75a23c03" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" version = "1.13.0" [[deps.TranscodingStreams]] deps = ["Random", "Test"] git-tree-sha1 = "9a6ae7ed916312b41236fcef7e0af564ef934769" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" version = "0.9.13" [[deps.TypedTables]] deps = ["Adapt", "Dictionaries", "Indexing", "SplitApplyCombine", "Tables", "Unicode"] git-tree-sha1 = "d911ae4e642cf7d56b1165d29ef0a96ba3444ca9" uuid = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9" version = "1.4.3" [[deps.UUIDs]] deps = ["Random", "SHA"] uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" [[deps.Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" version = "1.2.12+3" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] git-tree-sha1 = "49ce682769cd5de6c72dcf1b94ed7790cd08974c" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" version = "1.5.5+0" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" version = "5.1.1+0" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" version = "1.48.0+0" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" version = "17.4.0+0" i Starting Julia with 2 threads v Starting Julia with 2 threads [7.4s] i Activating package environment Precompiling project... ✓ JlmerClusterPerm 1 dependency successfully precompiled in 79 seconds. 110 already precompiled. v Activating package environment [1m 29s] i Running package setup scripts (1/11) i Running package setup scripts (7/11) i Running package setup scripts (9/11) ERROR: LoadError: UndefVarError: ByRow not defined Stacktrace: [1] include @ .\Base.jl:419 [inlined] [2] 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, UInt64}}, source::Nothing) @ Base .\loading.jl:1554 [3] top-level scope @ stdin:1 in expression starting at C:\Users\CRAN\.julia\packages\DataFrames\58MUJ\src\DataFrames.jl:1 in expression starting at stdin:1 x Running package setup scripts (9/11) [57.9s] ERROR: LoadError: UndefVarError: ByRow not defined Stacktrace: [1] include @ .\Base.jl:419 [inlined] [2] 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, UInt64}}, source::Nothing) @ Base .\loading.jl:1554 [3] top-level scope @ stdin:1 in expression starting at C:\Users\CRAN\.julia\packages\DataFrames\58MUJ\src\DataFrames.jl:1 in expression starting at stdin:1 [ FAIL 4 | WARN 0 | SKIP 7 | PASS 5 ] ══ Skipped tests (7) ═══════════════════════════════════════════════════════════ • On CRAN (7): 'test-jlmer.R:1:1', 'test-julia_rng.R:1:1', 'test-permute.R:1:1', 'test-progress.R:1:1', 'test-singularity.R:1:1', 'test-threshold_search.R:1:1', 'test-timewise_statistics.R:1:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-aaa-b-setup.R:11:3'): Setup with seed works (use 2 for testing) ── Error: Evaluation in Julia failed. Original Julia error message: LoadError: Failed to precompile DataFrames [a93c6f00-e57d-5684-b7b6-d8193f3e46c0] to C:\Users\CRAN\.julia\compiled\v1.8\DataFrames\jl_FC6D.tmp. Stacktrace: [1] error(s::String) @ Base .\error.jl:35 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool) @ Base .\loading.jl:1705 [3] compilecache @ .\loading.jl:1649 [inlined] [4] _require(pkg::Base.PkgId) @ Base .\loading.jl:1337 [5] _require_prelocked(uuidkey::Base.PkgId) @ Base .\loading.jl:1200 [6] macro expansion @ .\loading.jl:1180 [inlined] [7] macro expansion @ .\lock.jl:223 [inlined] [8] require(into::Module, mod::Symbol) @ Base .\loading.jl:1144 [9] eval @ .\boot.jl:368 [inlined] [10] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base .\loading.jl:1428 [11] include_string (repeats 2 times) @ .\loading.jl:1438 [inlined] [12] mainevalcmd(str::String) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\JuliaConnectoR\Julia\evaluating.jl:150 [13] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base .\essentials.jl:729 [14] invokelatest(::Any, ::Any, ::Vararg{Any}) @ Base .\essentials.jl:726 [15] evaluate!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\JuliaConnectoR\Julia\evaluating.jl:67 [16] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\JuliaConnectoR\Julia\evaluating.jl:55 [17] serve_repl(sock::Sockets.TCPSocket) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\JuliaConnectoR\Julia\communicating.jl:185 [18] (::Main.RConnector.var"#3#5")() @ Main.RConnector .\task.jl:484 in expression starting at string:1 Backtrace: ▆ 1. ├─testthat::expect_true(...) at test-aaa-b-setup.R:11:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─jlmerclusterperm::jlmerclusterperm_setup(...) 5. └─jlmerclusterperm:::setup_with_progress(...) 6. └─jlmerclusterperm:::source_jl(verbose = verbose) 7. └─JuliaConnectoR::juliaEval(jl_pkgs[i]) 8. └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr) 9. ├─base::tryCatch(...) 10. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 12. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 13. └─JuliaConnectoR:::doCallJulia(funName, jlargs) 14. └─JuliaConnectoR:::handleCallbacksAndOutput() ── Failure ('test-aaa-b-setup.R:17:3'): RNG initializes to seed=1 counter=0 ──── get_rng_seed() (`actual`) not equal to 1 (`expected`). `actual` is NULL `expected` is a double vector (1) ── Error ('test-aaa-b-setup.R:18:3'): RNG initializes to seed=1 counter=0 ────── Error: Evaluation in Julia failed. Original Julia error message: LoadError: UndefVarError: rng not defined Stacktrace: [1] top-level scope @ string:1 [2] eval @ .\boot.jl:368 [inlined] [3] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base .\loading.jl:1428 [4] include_string (repeats 2 times) @ .\loading.jl:1438 [inlined] [5] mainevalcmd(str::String) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\JuliaConnectoR\Julia\evaluating.jl:150 [6] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base .\essentials.jl:729 [7] invokelatest(::Any, ::Any, ::Vararg{Any}) @ Base .\essentials.jl:726 [8] evaluate!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\JuliaConnectoR\Julia\evaluating.jl:67 [9] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\JuliaConnectoR\Julia\evaluating.jl:55 [10] serve_repl(sock::Sockets.TCPSocket) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\JuliaConnectoR\Julia\communicating.jl:185 [11] (::Main.RConnector.var"#3#5")() @ Main.RConnector .\task.jl:484 in expression starting at string:1 Backtrace: ▆ 1. ├─testthat::expect_equal(get_rng_state(), 0) at test-aaa-b-setup.R:18:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─jlmerclusterperm::get_rng_state() 5. └─JuliaConnectoR::juliaEval("Int(rng.ctr1)") 6. └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr) 7. ├─base::tryCatch(...) 8. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 9. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 11. └─JuliaConnectoR:::doCallJulia(funName, jlargs) 12. └─JuliaConnectoR:::handleCallbacksAndOutput() ── Error ('test-clusterpermute.R:3:1'): (code run outside of `test_that()`) ──── Error: Evaluation in Julia failed. Original Julia error message: LoadError: Failed to precompile DataFrames [a93c6f00-e57d-5684-b7b6-d8193f3e46c0] to C:\Users\CRAN\.julia\compiled\v1.8\DataFrames\jl_2A8C.tmp. Stacktrace: [1] error(s::String) @ Base .\error.jl:35 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool) @ Base .\loading.jl:1705 [3] compilecache @ .\loading.jl:1649 [inlined] [4] _require(pkg::Base.PkgId) @ Base .\loading.jl:1337 [5] _require_prelocked(uuidkey::Base.PkgId) @ Base .\loading.jl:1200 [6] macro expansion @ .\loading.jl:1180 [inlined] [7] macro expansion @ .\lock.jl:223 [inlined] [8] require(into::Module, mod::Symbol) @ Base .\loading.jl:1144 [9] eval @ .\boot.jl:368 [inlined] [10] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base .\loading.jl:1428 [11] include_string (repeats 2 times) @ .\loading.jl:1438 [inlined] [12] mainevalcmd(str::String) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\JuliaConnectoR\Julia\evaluating.jl:150 [13] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base .\essentials.jl:729 [14] invokelatest(::Any, ::Any, ::Vararg{Any}) @ Base .\essentials.jl:726 [15] evaluate!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\JuliaConnectoR\Julia\evaluating.jl:67 [16] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\JuliaConnectoR\Julia\evaluating.jl:55 [17] serve_repl(sock::Sockets.TCPSocket) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\JuliaConnectoR\Julia\communicating.jl:185 [18] (::Main.RConnector.var"#3#5")() @ Main.RConnector .\task.jl:484 in expression starting at string:1 Backtrace: ▆ 1. └─jlmerclusterperm::jlmerclusterperm_setup(restart = FALSE, verbose = FALSE) at test-clusterpermute.R:3:1 2. └─jlmerclusterperm:::setup_with_progress(...) 3. └─jlmerclusterperm:::source_jl(verbose = verbose) 4. └─JuliaConnectoR::juliaEval(jl_pkgs[i]) 5. └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr) 6. ├─base::tryCatch(...) 7. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 8. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 9. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 10. └─JuliaConnectoR:::doCallJulia(funName, jlargs) 11. └─JuliaConnectoR:::handleCallbacksAndOutput() [ FAIL 4 | WARN 0 | SKIP 7 | PASS 5 ] Error: Test failures Execution halted Flavor: r-release-windows-x86_64

Version: 1.1.2
Check: tests
Result: ERROR Running 'testthat.R' [264s] Running the tests in 'tests/testthat.R' failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(jlmerclusterperm) > > test_check("jlmerclusterperm") Julia Version 1.8.0 Commit 5544a0fab7 (2022-08-17 13:38 UTC) Platform Info: OS: Windows (x86_64-w64-mingw32) CPU: 56 × Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-13.0.1 (ORCJIT, broadwell) Threads: 1 on 56 virtual cores nothing ℹ Starting Julia with 2 threads ✔ Starting Julia with 2 threads [7.5s] ℹ Activating package environment ✔ Activating package environment [16.2s] Status `C:\Users\CRAN\AppData\Local\R\cache\R\jlmerclusterperm\julia\Project.toml` [a93c6f00] DataFrames v1.6.1 [31c24e10] Distributions v0.25.103 [38e38edf] GLM v1.9.0 [2a59065a] JlmerClusterPerm v0.1.1 `JlmerClusterPerm` [ff71e718] MixedModels v4.22.2 [92933f4c] ProgressMeter v1.9.0 [74087812] Random123 v1.6.1 ⌃ [2913bbd2] StatsBase v0.33.21 [3eaba693] StatsModels v0.7.3 [fd094767] Suppressor v0.2.6 [9a3f8284] Random Info Packages marked with ⌃ have new versions available # This file is machine-generated - editing it directly is not advised julia_version = "1.8.0" manifest_format = "2.0" project_hash = "998a3e62f1f1411e2e150f96d1c48126701e35d7" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] git-tree-sha1 = "02f731463748db57cc2ebfbd9fbc9ce8280d3433" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" version = "3.7.1" [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" version = "1.1.1" [[deps.ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra", "SparseArrays"] git-tree-sha1 = "af43df5704827c8618afd36eb56fcab20d3041ee" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" version = "1.4.3" [[deps.Arrow]] deps = 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"IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] git-tree-sha1 = "f625d686d5a88bcd2b15cd81f18f98186fdc0c9a" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" version = "1.3.0" [[deps.StatsModels]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Printf", "REPL", "ShiftedArrays", "SparseArrays", "StatsAPI", "StatsBase", "StatsFuns", "Tables"] git-tree-sha1 = "5cf6c4583533ee38639f73b880f35fc85f2941e0" uuid = "3eaba693-59b7-5ba5-a881-562e759f1c8d" version = "0.7.3" [[deps.StringManipulation]] deps = ["PrecompileTools"] git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" version = "0.3.4" [[deps.StructTypes]] deps = ["Dates", "UUIDs"] git-tree-sha1 = "ca4bccb03acf9faaf4137a9abc1881ed1841aa70" uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4" version = "1.10.0" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" [[deps.Suppressor]] deps = ["Logging"] git-tree-sha1 = "6cd9e4a207964c07bf6395beff7a1e8f21d0f3b2" uuid = "fd094767-a336-5f1f-9728-57cf17d0bbfb" version = "0.2.6" [[deps.TOML]] deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" version = "1.0.0" [[deps.TZJData]] deps = ["Artifacts"] git-tree-sha1 = "d39314cdbaf5b90a047db33858626f8d1cc973e1" uuid = "dc5dba14-91b3-4cab-a142-028a31da12f7" version = "1.0.0+2023c" [[deps.TableTraits]] deps = ["IteratorInterfaceExtensions"] git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39" uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" version = "1.0.1" [[deps.Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits"] git-tree-sha1 = "cb76cf677714c095e535e3501ac7954732aeea2d" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" version = "1.11.1" [[deps.Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" version = "1.10.0" [[deps.Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.TimeZones]] deps = ["Artifacts", "Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "RecipesBase", "Scratch", "TZJData", "Unicode", "p7zip_jll"] git-tree-sha1 = "89e64d61ef3cd9e80f7fc12b7d13db2d75a23c03" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" version = "1.13.0" [[deps.TranscodingStreams]] deps = ["Random", "Test"] git-tree-sha1 = "9a6ae7ed916312b41236fcef7e0af564ef934769" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" version = "0.9.13" [[deps.TypedTables]] deps = ["Adapt", "Dictionaries", "Indexing", "SplitApplyCombine", "Tables", "Unicode"] git-tree-sha1 = "d911ae4e642cf7d56b1165d29ef0a96ba3444ca9" uuid = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9" version = "1.4.3" [[deps.UUIDs]] deps = ["Random", "SHA"] uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" [[deps.Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" version = "1.2.12+3" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] git-tree-sha1 = "49ce682769cd5de6c72dcf1b94ed7790cd08974c" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" version = "1.5.5+0" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" version = "5.1.1+0" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" version = "1.48.0+0" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" version = "17.4.0+0" i Starting Julia with 2 threads v Starting Julia with 2 threads [6.8s] i Activating package environment Precompiling project... ✓ JlmerClusterPerm 1 dependency successfully precompiled in 77 seconds. 110 already precompiled. v Activating package environment [1m 26.7s] i Running package setup scripts (1/11) i Running package setup scripts (4/11) i Running package setup scripts (7/11) i Running package setup scripts (9/11) ERROR: LoadError: UndefVarError: ByRow not defined Stacktrace: [1] include @ .\Base.jl:419 [inlined] [2] 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, UInt64}}, source::Nothing) @ Base .\loading.jl:1554 [3] top-level scope @ stdin:1 in expression starting at C:\Users\CRAN\.julia\packages\DataFrames\58MUJ\src\DataFrames.jl:1 in expression starting at stdin:1 x Running package setup scripts (9/11) [56.9s] ERROR: LoadError: UndefVarError: ByRow not defined Stacktrace: [1] include @ .\Base.jl:419 [inlined] [2] 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, UInt64}}, source::Nothing) @ Base .\loading.jl:1554 [3] top-level scope @ stdin:1 in expression starting at C:\Users\CRAN\.julia\packages\DataFrames\58MUJ\src\DataFrames.jl:1 in expression starting at stdin:1 [ FAIL 4 | WARN 0 | SKIP 7 | PASS 5 ] ══ Skipped tests (7) ═══════════════════════════════════════════════════════════ • On CRAN (7): 'test-jlmer.R:1:1', 'test-julia_rng.R:1:1', 'test-permute.R:1:1', 'test-progress.R:1:1', 'test-singularity.R:1:1', 'test-threshold_search.R:1:1', 'test-timewise_statistics.R:1:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-aaa-b-setup.R:11:3'): Setup with seed works (use 2 for testing) ── Error: Evaluation in Julia failed. Original Julia error message: LoadError: Failed to precompile DataFrames [a93c6f00-e57d-5684-b7b6-d8193f3e46c0] to C:\Users\CRAN\.julia\compiled\v1.8\DataFrames\jl_E944.tmp. Stacktrace: [1] error(s::String) @ Base .\error.jl:35 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool) @ Base .\loading.jl:1705 [3] compilecache @ .\loading.jl:1649 [inlined] [4] _require(pkg::Base.PkgId) @ Base .\loading.jl:1337 [5] _require_prelocked(uuidkey::Base.PkgId) @ Base .\loading.jl:1200 [6] macro expansion @ .\loading.jl:1180 [inlined] [7] macro expansion @ .\lock.jl:223 [inlined] [8] require(into::Module, mod::Symbol) @ Base .\loading.jl:1144 [9] eval @ .\boot.jl:368 [inlined] [10] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base .\loading.jl:1428 [11] include_string (repeats 2 times) @ .\loading.jl:1438 [inlined] [12] mainevalcmd(str::String) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.2\JuliaConnectoR\Julia\evaluating.jl:150 [13] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base .\essentials.jl:729 [14] invokelatest(::Any, ::Any, ::Vararg{Any}) @ Base .\essentials.jl:726 [15] evaluate!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.2\JuliaConnectoR\Julia\evaluating.jl:67 [16] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.2\JuliaConnectoR\Julia\evaluating.jl:55 [17] serve_repl(sock::Sockets.TCPSocket) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.2\JuliaConnectoR\Julia\communicating.jl:185 [18] (::Main.RConnector.var"#3#5")() @ Main.RConnector .\task.jl:484 in expression starting at string:1 Backtrace: ▆ 1. ├─testthat::expect_true(...) at test-aaa-b-setup.R:11:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─jlmerclusterperm::jlmerclusterperm_setup(...) 5. └─jlmerclusterperm:::setup_with_progress(...) 6. └─jlmerclusterperm:::source_jl(verbose = verbose) 7. └─JuliaConnectoR::juliaEval(jl_pkgs[i]) 8. └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr) 9. ├─base::tryCatch(...) 10. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 12. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 13. └─JuliaConnectoR:::doCallJulia(funName, jlargs) 14. └─JuliaConnectoR:::handleCallbacksAndOutput() ── Failure ('test-aaa-b-setup.R:17:3'): RNG initializes to seed=1 counter=0 ──── get_rng_seed() (`actual`) not equal to 1 (`expected`). `actual` is NULL `expected` is a double vector (1) ── Error ('test-aaa-b-setup.R:18:3'): RNG initializes to seed=1 counter=0 ────── Error: Evaluation in Julia failed. Original Julia error message: LoadError: UndefVarError: rng not defined Stacktrace: [1] top-level scope @ string:1 [2] eval @ .\boot.jl:368 [inlined] [3] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base .\loading.jl:1428 [4] include_string (repeats 2 times) @ .\loading.jl:1438 [inlined] [5] mainevalcmd(str::String) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.2\JuliaConnectoR\Julia\evaluating.jl:150 [6] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base .\essentials.jl:729 [7] invokelatest(::Any, ::Any, ::Vararg{Any}) @ Base .\essentials.jl:726 [8] evaluate!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.2\JuliaConnectoR\Julia\evaluating.jl:67 [9] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.2\JuliaConnectoR\Julia\evaluating.jl:55 [10] serve_repl(sock::Sockets.TCPSocket) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.2\JuliaConnectoR\Julia\communicating.jl:185 [11] (::Main.RConnector.var"#3#5")() @ Main.RConnector .\task.jl:484 in expression starting at string:1 Backtrace: ▆ 1. ├─testthat::expect_equal(get_rng_state(), 0) at test-aaa-b-setup.R:18:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─jlmerclusterperm::get_rng_state() 5. └─JuliaConnectoR::juliaEval("Int(rng.ctr1)") 6. └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr) 7. ├─base::tryCatch(...) 8. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 9. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 11. └─JuliaConnectoR:::doCallJulia(funName, jlargs) 12. └─JuliaConnectoR:::handleCallbacksAndOutput() ── Error ('test-clusterpermute.R:3:1'): (code run outside of `test_that()`) ──── Error: Evaluation in Julia failed. Original Julia error message: LoadError: Failed to precompile DataFrames [a93c6f00-e57d-5684-b7b6-d8193f3e46c0] to C:\Users\CRAN\.julia\compiled\v1.8\DataFrames\jl_188C.tmp. Stacktrace: [1] error(s::String) @ Base .\error.jl:35 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool) @ Base .\loading.jl:1705 [3] compilecache @ .\loading.jl:1649 [inlined] [4] _require(pkg::Base.PkgId) @ Base .\loading.jl:1337 [5] _require_prelocked(uuidkey::Base.PkgId) @ Base .\loading.jl:1200 [6] macro expansion @ .\loading.jl:1180 [inlined] [7] macro expansion @ .\lock.jl:223 [inlined] [8] require(into::Module, mod::Symbol) @ Base .\loading.jl:1144 [9] eval @ .\boot.jl:368 [inlined] [10] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base .\loading.jl:1428 [11] include_string (repeats 2 times) @ .\loading.jl:1438 [inlined] [12] mainevalcmd(str::String) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.2\JuliaConnectoR\Julia\evaluating.jl:150 [13] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base .\essentials.jl:729 [14] invokelatest(::Any, ::Any, ::Vararg{Any}) @ Base .\essentials.jl:726 [15] evaluate!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.2\JuliaConnectoR\Julia\evaluating.jl:67 [16] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.2\JuliaConnectoR\Julia\evaluating.jl:55 [17] serve_repl(sock::Sockets.TCPSocket) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.2\JuliaConnectoR\Julia\communicating.jl:185 [18] (::Main.RConnector.var"#3#5")() @ Main.RConnector .\task.jl:484 in expression starting at string:1 Backtrace: ▆ 1. └─jlmerclusterperm::jlmerclusterperm_setup(restart = FALSE, verbose = FALSE) at test-clusterpermute.R:3:1 2. └─jlmerclusterperm:::setup_with_progress(...) 3. └─jlmerclusterperm:::source_jl(verbose = verbose) 4. └─JuliaConnectoR::juliaEval(jl_pkgs[i]) 5. └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr) 6. ├─base::tryCatch(...) 7. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 8. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 9. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 10. └─JuliaConnectoR:::doCallJulia(funName, jlargs) 11. └─JuliaConnectoR:::handleCallbacksAndOutput() [ FAIL 4 | WARN 0 | SKIP 7 | PASS 5 ] Error: Test failures Execution halted Flavor: r-oldrel-windows-x86_64