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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:DFplyr.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings DFplyr_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/DFplyr.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘DFplyr/DESCRIPTION’ ... OK
* this is package ‘DFplyr’ version ‘1.4.0’
* 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 ‘DFplyr’ 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 ... OK
* 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 ‘DFplyr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summarise.DataFrame
> ### Title: Summarise each group down to one row
> ### Aliases: summarise.DataFrame
> 
> ### ** Examples
> 
> # A summary applied to ungrouped tbl returns a single row
> mtcars %>%
+   summarise(mean = mean(disp), n = n())
      mean  n
1 230.7219 32
> 
> # Usually, you'll want to group first
> mtcars %>%
+   group_by(cyl) %>%
+   summarise(mean = mean(disp), n = n())
# A tibble: 3 × 3
    cyl  mean     n
  <dbl> <dbl> <int>
1     4  105.    11
2     6  183.     7
3     8  353.    14
> 
> # Each summary call removes one grouping level (since that group
> # is now just a single row)
> mtcars %>%
+   group_by(cyl, vs) %>%
+   summarise(cyl_n = n()) %>%
+   group_vars()
`summarise()` has regrouped the output.
ℹ Summaries were computed grouped by cyl and vs.
ℹ Output is grouped by cyl.
ℹ Use `summarise(.groups = "drop_last")` to silence this message.
ℹ Use `summarise(.by = c(cyl, vs))` for per-operation grouping
  (`?dplyr::dplyr_by`) instead.
[1] "cyl"
> 
> # BEWARE: reusing variables may lead to unexpected results
> mtcars %>%
+   group_by(cyl) %>%
+   summarise(disp = mean(disp), sd = sd(disp))
# A tibble: 3 × 3
    cyl  disp    sd
  <dbl> <dbl> <dbl>
1     4  105.    NA
2     6  183.    NA
3     8  353.    NA
> 
> # Refer to column names stored as strings with the `.data` pronoun:
> var <- "mass"
> summarise(starwars, avg = mean(.data[[var]], na.rm = TRUE))
# A tibble: 1 × 1
    avg
  <dbl>
1  97.3
> # Learn more in ?rlang::args_data_masking
> 
> # In dplyr 1.1.0, returning multiple rows per group was deprecated in favor
> # of `reframe()`, which never messages and always returns an ungrouped
> # result:
> mtcars %>%
+    group_by(cyl) %>%
+    summarise(qs = quantile(disp, c(0.25, 0.75)), prob = c(0.25, 0.75))
Error in `summarise()`:
ℹ In argument: `qs = quantile(disp, c(0.25, 0.75))`.
ℹ In group 1: `cyl = 4`.
Caused by error:
! `qs` must be size 1, not 2.
ℹ To return more or less than 1 row per group, use `reframe()`.
Backtrace:
     ▆
  1. ├─mtcars %>% group_by(cyl) %>% ...
  2. ├─dplyr::summarise(...)
  3. ├─dplyr:::summarise.grouped_df(., qs = quantile(disp, c(0.25, 0.75)), prob = c(0.25, 0.75))
  4. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
  5. │   └─base::withCallingHandlers(...)
  6. ├─dplyr:::dplyr_internal_error(...)
  7. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
  8. │   └─rlang:::signal_abort(cnd, .file)
  9. │     └─base::signalCondition(cnd)
 10. └─dplyr (local) `<fn>`(`<dpl:::__>`)
 11.   └─dplyr (local) handler(cnd)
 12.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/DFplyr.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL DFplyr
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘DFplyr’ ...
** this is package ‘DFplyr’ version ‘1.4.0’
** using staged installation
** R
** 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 (DFplyr)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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.

> # 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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(DFplyr)
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'DFplyr'

The following object is masked from 'package:dplyr':

    desc

> 
> test_check("DFplyr")
Joining with `by = join_by(name, eye_color)`
Joining with `by = join_by(name, eye_color)`
Joining with `by = join_by(name, eye_color)`
Joining with `by = join_by(name, eye_color)`
Joining with `by = c("name", "eye_color")`
Joining with `by = c("name", "eye_color")`
Joining with `by = c("name", "eye_color")`
Joining with `by = c("name", "eye_color")`
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 105 ]
> 
> proc.time()
   user  system elapsed 
 11.429   0.689  12.111