CRAN Package Check Results for Package LongDat

Last updated on 2022-07-07 05:56:05 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.5 20.71 210.05 230.76 OK
r-devel-linux-x86_64-debian-gcc 1.0.5 17.70 153.02 170.72 NOTE
r-devel-linux-x86_64-fedora-clang 1.0.5 280.63 OK
r-devel-linux-x86_64-fedora-gcc 1.0.5 274.24 OK
r-devel-windows-x86_64 1.0.5 28.00 234.00 262.00 NOTE
r-patched-linux-x86_64 1.0.5 17.25 197.19 214.44 OK
r-release-linux-x86_64 1.0.5 18.75 196.93 215.68 OK
r-release-macos-arm64 1.0.5 56.00 ERROR
r-release-macos-x86_64 1.0.5 101.00 OK
r-release-windows-x86_64 1.0.5 45.00 230.00 275.00 OK
r-oldrel-macos-arm64 1.0.5 64.00 OK
r-oldrel-macos-x86_64 1.0.5 101.00 OK
r-oldrel-windows-ix86+x86_64 1.0.5 46.00 235.00 281.00 OK

Check Details

Version: 1.0.5
Check: package subdirectories
Result: NOTE
    Problems with news in ‘NEWS.md’:
    No news entries found.
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64

Version: 1.0.5
Check: examples
Result: ERROR
    Running examples in ‘LongDat-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: cuneiform_plot
    > ### Title: Create cuneiform plots of result table from longdat_disc() or
    > ### longdat_cont()
    > ### Aliases: cuneiform_plot
    >
    > ### ** Examples
    >
    > test_disc <- longdat_disc(input = LongDat_disc_master_table,
    + data_type = "count", test_var = "Time_point",
    + variable_col = 7, fac_var = c(1:3))
    [1] "Start data preprocessing."
    [1] "Finish data preprocessing."
    [1] "Start selecting potential covariates."
    [1] 1
    [1] 2
    [1] 3
    [1] 1
    [1] 2
    [1] 3
    [1] "Finished selecting potential covariates."
    [1] "Start null model test and post-hoc test."
    [1] 1
    ERROR : Incorrect number of arguments (4), expecting 3 for 'getParameterOrder'
    [1] 2
    ERROR : Incorrect number of arguments (4), expecting 3 for 'getParameterOrder'
    [1] 3
    ERROR : Incorrect number of arguments (4), expecting 3 for 'getParameterOrder'
    [1] "Finish null model test and post-hoc test."
    [1] "Start covariate model test."
    [1] 1
    ERROR : Incorrect number of arguments (4), expecting 3 for 'getParameterOrder'
    [1] 2
    [1] 3
    [1] "Finish covariate model test."
    [1] "Start unlisting tables from covariate model result."
    Using p_lm as value column: use value.var to override.
    Using p_lm as value column: use value.var to override.
    [1] "Finish unlisting tables from covariate model result."
    [1] "Start calculating effect size."
    [1] 1
    [1] 2
    [1] 3
    [1] "Finish calculating effect size."
    [1] "Start randomized negative control model test."
    [1] 1
    ERROR : Incorrect number of arguments (4), expecting 3 for 'getParameterOrder'
    [1] 2
    ERROR : Incorrect number of arguments (4), expecting 3 for 'getParameterOrder'
    [1] 3
    ERROR : Incorrect number of arguments (4), expecting 3 for 'getParameterOrder'
    [1] 1
    [1] 2
    [1] 3
    Error in eval(e, x, parent.frame()) : object 'NB_theta' not found
    Calls: longdat_disc ... random_neg_ctrl_disc -> subset -> subset.data.frame -> eval -> eval
    Execution halted
Flavor: r-release-macos-arm64

Version: 1.0.5
Check: re-building of vignette outputs
Result: ERROR
    Error(s) in re-building vignettes:
    --- re-building ‘LongDat_cont_tutorial.Rmd’ using rmarkdown
    Warning in checkDepPackageVersion(dep_pkg = "TMB") :
     Package version inconsistency detected.
    glmmTMB was built with TMB version 1.7.22
    Current TMB version is 1.9.0
    Please re-install glmmTMB from source or restore original 'TMB' package (see '?reinstalling' for more information)
    ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
    ✔ ggplot2 3.3.6 ✔ purrr 0.3.4
    ✔ tibble 3.1.7 ✔ dplyr 1.0.9
    ✔ tidyr 1.2.0 ✔ stringr 1.4.0
    ✔ readr 2.1.2 ✔ forcats 0.5.1
    ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
    ✖ dplyr::filter() masks stats::filter()
    ✖ dplyr::lag() masks stats::lag()
    
    Attaching package: 'kableExtra'
    
    The following object is masked from 'package:dplyr':
    
     group_rows
    
    Using p_lm as value column: use value.var to override.
    Using p_lm as value column: use value.var to override.
    Warning in cor.test.default(subdata[, test_var], subdata$value, method = "spearman") :
     Cannot compute exact p-value with ties
    Warning in cor.test.default(subdata[, test_var], subdata$value, method = "spearman") :
     Cannot compute exact p-value with ties
    Warning in cor.test.default(subdata[, test_var], subdata$value, method = "spearman") :
     Cannot compute exact p-value with ties
    Warning in cor.test.default(subdata_random[, test_var], subdata_random$value, :
     Cannot compute exact p-value with ties
    Warning in cor.test.default(subdata_random[, test_var], subdata_random$value, :
     Cannot compute exact p-value with ties
    Warning in cor.test.default(subdata_random[, test_var], subdata_random$value, :
     Cannot compute exact p-value with ties
    Quitting from lines 109-116 (LongDat_cont_tutorial.Rmd)
    Error: processing vignette 'LongDat_cont_tutorial.Rmd' failed with diagnostics:
    object 'NB_theta' not found
    --- failed re-building ‘LongDat_cont_tutorial.Rmd’
    
    --- re-building ‘LongDat_disc_tutorial.Rmd’ using rmarkdown
    Using p_lm as value column: use value.var to override.
    Using p_lm as value column: use value.var to override.
    Quitting from lines 109-116 (LongDat_disc_tutorial.Rmd)
    Error: processing vignette 'LongDat_disc_tutorial.Rmd' failed with diagnostics:
    object 'NB_theta' not found
    --- failed re-building ‘LongDat_disc_tutorial.Rmd’
    
    SUMMARY: processing the following files failed:
     ‘LongDat_cont_tutorial.Rmd’ ‘LongDat_disc_tutorial.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-macos-arm64