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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:plotGrouper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings plotGrouper_1.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/plotGrouper.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘plotGrouper/DESCRIPTION’ ... OK
* this is package ‘plotGrouper’ version ‘1.29.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘plotGrouper’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
gplot: no visible binding for global variable ‘max_value’
gplot: no visible binding for global variable ‘max_error’
Undefined global functions or variables:
  max_error max_value
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘plotGrouper-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gplot
> ### Title: A function to create a grouped plot and return a table grob.
> ### Aliases: gplot
> 
> ### ** Examples
> 
> iris %>% dplyr::mutate(Species = as.character(Species)) %>%
+ dplyr::group_by(Species) %>%
+ dplyr::mutate(Sample = paste0(Species, "_", dplyr::row_number()),
+ Sheet = "iris") %>%
+ dplyr::select(Sample, Sheet, Species, dplyr::everything()) %>%
+ tidyr::gather(variable, value, -c(Sample, Sheet, Species)) %>%
+ dplyr::filter(variable == "Sepal.Length") %>%
+ plotGrouper::gplot(
+ comparison = "Species",
+ group.by = "variable",
+ shape.groups = c(19,21,17),
+ color.groups = c(rep("black",3)),
+ fill.groups = c("black","#E016BE", "#1243C9")) %>%
+ gridExtra::grid.arrange()
Error:
! `arrange_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `arrange()` instead.
ℹ See vignette('programming') for more help
Backtrace:
    ▆
 1. ├─... %>% gridExtra::grid.arrange()
 2. ├─gridExtra::grid.arrange(.)
 3. │ └─gridExtra::arrangeGrob(...)
 4. └─plotGrouper::gplot(...)
 5.   └─dplyr::arrange_(df, comparison)
 6.     └─dplyr:::lazy_defunct("arrange")
 7.       └─lifecycle::deprecate_stop(...)
 8.         └─lifecycle:::deprecate_stop0(msg)
 9.           └─rlang::cnd_signal(...)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ℹ See vignette('programming') for more help
  Backtrace:
      ▆
   1. ├─... %>% ... at test-gplot.R:6:3
   2. └─plotGrouper::gplot(...)
   3.   └─dplyr::arrange_(df, comparison)
   4.     └─dplyr:::lazy_defunct("arrange")
   5.       └─lifecycle::deprecate_stop(...)
   6.         └─lifecycle:::deprecate_stop0(msg)
   7.           └─rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 3 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/plotGrouper.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL plotGrouper
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘plotGrouper’ ...
** this is package ‘plotGrouper’ version ‘1.29.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (plotGrouper)

R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(plotGrouper)
> 
> test_check("plotGrouper")
Saving _problems/test-gplot-26.R
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 3 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-gplot.R:6:3'): gplot works ─────────────────────────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: `arrange_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `arrange()` instead.
ℹ See vignette('programming') for more help
Backtrace:
    ▆
 1. ├─... %>% ... at test-gplot.R:6:3
 2. └─plotGrouper::gplot(...)
 3.   └─dplyr::arrange_(df, comparison)
 4.     └─dplyr:::lazy_defunct("arrange")
 5.       └─lifecycle::deprecate_stop(...)
 6.         └─lifecycle:::deprecate_stop0(msg)
 7.           └─rlang::cnd_signal(...)

[ FAIL 1 | WARN 2 | SKIP 0 | PASS 3 ]
Error:
! Test failures.
Execution halted