CRAN Package Check Results for Package jlmerclusterperm

Last updated on 2024-12-24 20:49:22 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1.4 3.43 36.88 40.31 OK
r-devel-linux-x86_64-debian-gcc 1.1.4 2.24 29.09 31.33 OK
r-devel-linux-x86_64-fedora-clang 1.1.4 67.55 OK
r-devel-linux-x86_64-fedora-gcc 1.1.4 78.43 OK
r-devel-windows-x86_64 1.1.4 5.00 656.00 661.00 OK
r-patched-linux-x86_64 1.1.4 3.01 35.83 38.84 OK
r-release-linux-x86_64 1.1.4 3.07 34.94 38.01 OK
r-release-macos-arm64 1.1.4 46.00 OK
r-release-macos-x86_64 1.1.4 104.00 OK
r-release-windows-x86_64 1.1.4 5.00 869.00 874.00 ERROR
r-oldrel-macos-arm64 1.1.4 46.00 OK
r-oldrel-macos-x86_64 1.1.4 57.00 OK
r-oldrel-windows-x86_64 1.1.4 5.00 1014.00 1019.00 OK

Check Details

Version: 1.1.4
Check: tests
Result: ERROR Running 'testthat.R' [13m] 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 1.8.5 Commit 17cfb8e65e (2023-01-08 06:45 UTC) Platform Info: OS: Windows (x86_64-w64-mingw32) CPU: 48 × AMD EPYC 7443 24-Core Processor WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-13.0.1 (ORCJIT, znver3) Threads: 1 on 96 virtual cores nothing ℹ Starting Julia with 2 threads ✔ Starting Julia with 2 threads [5.1s] ℹ Activating package environment ✖ Activating package environment [14.7s] i Starting Julia with 2 threads v Starting Julia with 2 threads [5.1s] i Activating package environment Precompiling project... ✓ TZJData ✓ TimeZones ✓ StaticArrays ✓ FastGaussQuadrature ✓ ForwardDiff ✓ Arrow ✓ MixedModelsDatasets ✓ BSplineKit ✓ MathOptInterface ✓ NLopt ✓ MixedModels ✓ JlmerClusterPerm 12 dependencies successfully precompiled in 342 seconds. 97 already precompiled. v Activating package environment [5m 47.3s] i Running package setup scripts (1/11) i Running package setup scripts (6/11) i Running package setup scripts (9/11) i Running package setup scripts (11/11) v Running package setup scripts (11/11) [6m 13.3s] Julia instance already running - skipping setup. Progress: 2%|█ | ETA: 0:02:26 ( 1.49 s/it) Progress: 100%|████████████████████████████████████| Time: 0:00:03 (37.81 ms/it) Progress: 38%|██████████████ | ETA: 0:00:00 ( 3.71 ms/it) Progress: 100%|████████████████████████████████████| Time: 0:00:00 ( 2.04 ms/it) Progress: 85%|███████████████████████████████ | ETA: 0:00:00 ( 1.28 ms/it) Progress: 100%|████████████████████████████████████| Time: 0:00:00 ( 1.25 ms/it) i Detecting empirical clusters and calculating cluster-mass statistics. v Detecting empirical clusters and calculating cluster-mass statistics. [1.5s] i Sampling cluster-mass statistics from a bootstrapped null distribution. x Sampling cluster-mass statistics from a bootstrapped null distribution. [63... ── jlmer specification ───────────────────────────────────────── <jlmer_spec> ── Formula: weight ~ 1 + Diet2 + Diet3 + Diet4 Predictors: Diet: Diet2, Diet3, Diet4 Groupings: Subject: Chick Trial: Time: Time Data: weight Diet2 Diet3 Diet4 Chick Time 1 42 0 0 0 1 0 2 51 0 0 0 1 2 3 59 0 0 0 1 4 [ reached 'max' / getOption("max.print") -- omitted 530 rows ] ──────────────────────────────────────────────────────────────────────────────── Time Predictor 0 2 4 6 8 10 12 Diet2 -1.602704 1.670228 2.600323 3.520818 2.375235 1.909022 1.943661 Diet3 -1.373747 2.447078 4.476505 4.543060 3.699665 2.971831 3.061704 Diet4 -0.915831 3.534669 6.274514 6.996441 5.122934 4.071714 3.659132 Time Predictor 14 16 18 20 Diet2 1.341161 1.157799 1.396368 1.512195 Diet3 2.978569 3.045802 3.600737 3.802734 Diet4 2.782950 2.156651 2.134394 2.637206 ── Empirical clusters (t > 2) ────────────────────────── <empirical_clusters> ── Diet2 [4, 8]: 8.496 Diet3 [2, 20]: 34.628 Diet4 [2, 20]: 39.371 ──────────────────────────────────────────────────────────────────────────────── , , Predictor = Diet2 Time Sim 0 2 4 6 8 001 -8.976037e-01 4.123460e-01 3.905987e-01 1.118511261 1.58164911 002 1.395382e+00 9.029226e-01 9.591265e-01 1.437787960 1.60979028 003 -1.441907e+00 1.230785e+00 7.291090e-01 0.881170292 0.93375366 004 -4.488018e-01 1.107810e+00 3.456212e-01 -0.271478188 -0.10333453 005 1.383237e+00 1.027822e-01 6.161440e-01 -0.061358351 -0.30192831 006 -6.916186e-01 6.841944e-02 -3.063436e-01 -0.518037799 -0.20166941 007 1.128978e-01 -7.634112e-01 -5.636450e-01 -0.099694602 -0.02389785 008 3.337366e-01 2.086295e-01 3.313377e-01 -0.016467001 0.42453227 009 5.580322e-01 -1.035661e+00 -3.725952e-01 -0.156318773 0.36055944 010 -4.488018e-01 -2.809331e-01 2.011297e-01 0.485581918 0.42049224 011 1.359870e+00 3.444050e-02 3.189146e-01 0.562537475 0.20063217 012 4.532900e-01 -3.509829e-02 1.969140e-01 -0.436417760 0.34368723 013 -5.607722e-01 1.655750e+00 2.087875e+00 2.160581790 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1.507087708 0.93826624 086 0.849612945 1.270325965 1.45598406 1.741167471 1.63192063 087 -0.576163674 -0.588189114 -0.72281183 -0.331882203 -0.40732265 088 0.173954153 0.189400824 0.35690580 0.279925493 0.33910597 089 -0.248749994 -0.155633963 -0.36955917 -0.279642593 -0.43873719 090 0.668202462 0.723229063 0.56926766 0.630070392 0.52733653 091 -1.435460889 -1.467510453 -1.54204293 -0.970967799 -1.21950603 092 -0.059797489 -0.251202912 -0.35429428 -0.708829614 -0.89062698 093 -0.649207684 -0.581276123 -0.61016635 -0.410387530 -0.11483114 094 0.020848911 0.415373248 0.34788960 0.333223077 0.30543615 095 0.058568168 0.101197575 0.67670067 0.593655139 0.49570509 096 0.600781290 0.973971021 0.79543210 1.031313043 1.43026711 097 -0.540768177 -0.448100040 -0.38638089 -0.282141202 -0.13780282 098 1.932862589 1.882096456 1.74758782 1.717560322 1.78716848 099 0.040997891 0.358590214 1.13288182 0.739317398 0.75072004 100 0.952727472 0.633400444 0.24678906 0.515000508 0.31424097 Time Sim 20 001 -0.16397086 002 -0.42658337 003 0.52549566 004 0.16755230 005 1.18256511 006 0.57134286 007 1.66799478 008 0.75761986 009 1.58337474 010 -0.90411743 011 0.20315759 012 0.33112609 013 0.34189982 014 -0.28788783 015 -1.21863492 016 0.70462938 017 0.02019475 018 0.02973891 019 -0.21367098 020 1.04171654 021 0.09134416 022 -1.50000156 023 -0.15619143 024 -0.38922404 025 -0.72160652 026 1.44414530 027 1.00446581 028 -1.17275445 029 0.62144387 030 -0.31788501 031 -0.89210653 032 0.66733630 033 -0.42132791 034 -0.13109234 035 -0.05894552 036 -0.12586873 037 -0.26440591 038 0.41941538 039 -0.89546565 040 0.11223066 041 0.44644623 042 0.54513317 043 -0.62044054 044 -0.39687870 045 -1.43455324 046 -0.66178331 047 -0.24057519 048 1.00402315 049 0.23397764 050 0.86486364 051 0.12674842 052 -0.80786680 053 -2.74996702 054 -0.52554355 055 0.28782076 056 -0.99348207 057 0.57497163 058 -0.19327720 059 0.30789402 060 -0.10245198 061 -0.39249894 062 -0.53678202 063 -1.52074721 064 1.98159848 065 0.52564390 066 -0.20293235 067 0.33381717 068 0.77403228 069 -1.02377225 070 -0.01580273 071 1.93618723 072 -1.15763253 073 0.20798909 074 0.96682699 075 1.27654491 076 0.19620103 077 -1.82116475 078 1.25026390 079 0.21731885 080 -0.86089346 081 -0.16280049 082 1.70525214 083 -0.71715135 084 -0.72588414 085 0.82283265 086 1.60202029 087 -0.63153212 088 0.89872398 089 -0.22407346 090 0.19860300 091 -0.78538453 092 -0.75734545 093 -0.22627456 094 0.42197005 095 0.34639192 096 1.45693550 097 -0.09435302 098 1.65463396 099 0.57357761 100 0.24706215 ── Null cluster-mass distribution (t > 2) ────────────── <null_cluster_dists> ── Diet2 (n = 100) Mean (SD): 0.266 (2.13) Coverage intervals: 95% [0.000, 6.579] Diet3 (n = 100) Mean (SD): -0.124 (2.75) Coverage intervals: 95% [-4.777, 5.707] Diet4 (n = 100) Mean (SD): 0.007 (2.50) Coverage intervals: 95% [0.000, 0.000] ──────────────────────────────────────────────────────────────────────────────── ── Empirical clusters (t > 2) ────────────────────────── <empirical_clusters> ── Diet2 [4, 8]: 8.496 (p=0.0297) Diet3 [2, 20]: 34.628 (p=0.0099) Diet4 [2, 20]: 39.371 (p=0.0099) ──────────────────────────────────────────────────────────────────────────────── $null_cluster_dists ── Null cluster-mass distribution (t > 2) ────────────── <null_cluster_dists> ── Diet2 (n = 100) Mean (SD): 0.266 (2.13) Coverage intervals: 95% [0.000, 6.579] Diet3 (n = 100) Mean (SD): -0.124 (2.75) Coverage intervals: 95% [-4.777, 5.707] Diet4 (n = 100) Mean (SD): 0.007 (2.50) Coverage intervals: 95% [0.000, 0.000] ──────────────────────────────────────────────────────────────────────────────── $empirical_clusters ── Empirical clusters (t > 2) ────────────────────────── <empirical_clusters> ── Diet2 [4, 8]: 8.496 (p=0.0297) Diet3 [2, 20]: 34.628 (p=0.0099) Diet4 [2, 20]: 39.371 (p=0.0099) ──────────────────────────────────────────────────────────────────────────────── [ FAIL 1 | WARN 0 | SKIP 7 | PASS 20 ] ══ 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-a-logging.R:7:1'): (code run outside of `test_that()`) ───── Error: Evaluation in Julia failed. Original Julia error message: LoadError: Error when installing package TZJData: IOError: readdir("C:\\Users\\CRAN\\.julia\\packages\\TZJData\\CKNZV\\gen"): no such file or directory (ENOENT) Stacktrace: [1] try_yieldto(undo::typeof(Base.ensure_rescheduled)) @ Base .\task.jl:871 [2] wait() @ Base .\task.jl:931 [3] wait(c::Base.GenericCondition{ReentrantLock}) @ Base .\condition.jl:124 [4] take_unbuffered(c::Channel{Tuple{String, Vector{String}, Vector{String}}}) @ Base .\channels.jl:433 [5] take! @ .\channels.jl:410 [inlined] [6] iterate(c::Channel{Tuple{String, Vector{String}, Vector{String}}}, state::Nothing) @ Base .\channels.jl:498 [7] set_readonly(path::String) @ Pkg C:\PROGRA~1\Julia\share\julia\stdlib\v1.8\Pkg\src\utils.jl:54 [8] macro expansion @ C:\PROGRA~1\Julia\share\julia\stdlib\v1.8\Pkg\src\Operations.jl:763 [inlined] [9] (::Pkg.Operations.var"#46#51"{Bool, Pkg.Types.Context, Tuple{SubString{String}, Dict{Base.UUID, Base.SHA1}}, Channel{Any}, Channel{NamedTuple{(:pkg, :urls, :path), Tuple{Pkg.Types.PackageEntry, Set{String}, String}}}})() @ Pkg.Operations .\task.jl:484 Stacktrace: [1] pkgerror(::String, ::Vararg{String}) @ Pkg.Types C:\PROGRA~1\Julia\share\julia\stdlib\v1.8\Pkg\src\Types.jl:67 [2] macro expansion @ C:\PROGRA~1\Julia\share\julia\stdlib\v1.8\Pkg\src\Operations.jl:783 [inlined] [3] macro expansion @ .\task.jl:454 [inlined] [4] download_source(ctx::Pkg.Types.Context; readonly::Bool) @ Pkg.Operations C:\PROGRA~1\Julia\share\julia\stdlib\v1.8\Pkg\src\Operations.jl:724 [5] download_source @ C:\PROGRA~1\Julia\share\julia\stdlib\v1.8\Pkg\src\Operations.jl:700 [inlined] [6] develop(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, new_git::Set{Base.UUID}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform) @ Pkg.Operations C:\PROGRA~1\Julia\share\julia\stdlib\v1.8\Pkg\src\Operations.jl:1300 [7] develop(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; shared::Bool, preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, kwargs::Base.Pairs{Symbol, Base.DevNull, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.DevNull}}}) @ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.8\Pkg\src\API.jl:222 [8] develop(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.DevNull, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.8\Pkg\src\API.jl:156 [9] #develop#14 @ C:\PROGRA~1\Julia\share\julia\stdlib\v1.8\Pkg\src\API.jl:143 [inlined] [10] develop(; name::Nothing, uuid::Nothing, version::Nothing, url::Nothing, rev::Nothing, path::String, mode::Pkg.Types.PackageMode, subdir::Nothing, kwargs::Base.Pairs{Symbol, Base.DevNull, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.DevNull}}}) @ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.8\Pkg\src\API.jl:173 [11] top-level scope @ string:1 [12] eval @ .\boot.jl:368 [inlined] [13] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base .\loading.jl:1428 [14] include_string (repeats 2 times) @ .\loading.jl:1438 [inlined] [15] mainevalcmd(str::String) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\evaluating.jl:150 [16] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base .\essentials.jl:729 [17] invokelatest(::Any, ::Any, ::Vararg{Any}) @ Base .\essentials.jl:726 [18] evaluate!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\evaluating.jl:67 [19] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\evaluating.jl:55 [20] serve_repl(sock::Sockets.TCPSocket) @ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\communicating.jl:185 [21] (::Main.RConnector.var"#3#5")() @ Main.RConnector .\task.jl:484 in expression starting at string:1 Backtrace: ▆ 1. └─jlmerclusterperm:::set_projenv(cache_dir = tempdir(), verbose = TRUE) at test-aaa-a-logging.R:7:1 2. └─JuliaConnectoR::juliaEval("Pkg.develop(path = \"JlmerClusterPerm\", io = devnull)") 3. └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr) 4. ├─base::tryCatch(...) 5. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 6. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 7. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 8. └─JuliaConnectoR:::doCallJulia(funName, jlargs) 9. └─JuliaConnectoR:::handleCallbacksAndOutput() [ FAIL 1 | WARN 0 | SKIP 7 | PASS 20 ] Error: Test failures Execution halted Flavor: r-release-windows-x86_64