* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/qwraps2.Rcheck’
* using R Under development (unstable) (2026-06-11 r90128)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
    GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* current time: 2026-06-11 07:31:44 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘qwraps2/DESCRIPTION’ ... OK
* this is package ‘qwraps2’ version ‘0.6.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘rbenchmark’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘qwraps2’ can be installed ... [47s/30s] OK
* used C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
* 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 use of S3 registration ... 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 ... [12s/12s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘qwraps2-Ex.R’ failed
The error most likely occurred in:

> ### Name: logit
> ### Title: logit and inverse logit functions
> ### Aliases: logit invlogit
> 
> ### ** Examples
> 
> library(rbenchmark)
Error in library(rbenchmark) : there is no package called ‘rbenchmark’
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-confusion_matrix.R’
  Running ‘test-datasets.R’
  Running ‘test-extract.R’
  Running ‘test-file-check.R’
  Running ‘test-frmt.R’
  Running ‘test-frmtp.R’
  Running ‘test-gmean_sd.R’
  Running ‘test-lazyload.R’
  Running ‘test-ll.R’
  Running ‘test-logit.R’
  Running ‘test-mean_ci.R’
  Running ‘test-mean_sd.R’
  Running ‘test-mean_se.R’
  Running ‘test-median_iqr.R’
  Running ‘test-n_perc.R’
  Running ‘test-pkg_check.R’
  Running ‘test-plots.R’ [14s/14s]
  Running ‘test-qable.R’
  Running ‘test-qkplot.R’
  Running ‘test-qroc.R’
  Running ‘test-set_diff.R’
  Running ‘test-spin_comments.R’
  Running ‘test-summary_table.R’
  Running ‘test-traprule.R’
  Running ‘test-utilities.R’
 [26s/27s] ERROR
Running the tests in ‘tests/test-plots.R’ failed.
Complete output:
  > library(qwraps2)
  > 
  > # it is very difficult to build good tests for plots as the rendered plot needs
  > # to viewed by a human.  These tests are just to make sure that the underlying
  > # code is generating the same basic thing.  A human inspection of the examples
  > # and vignettes is highly recommended.
  > #
  > # This testing script can be thought of as a sneaky way to get the examples for
  > # plots into the code coverage based on only tests.
  > 
  > ################################################################################
  > #                                extract legend                                #
  > e <- new.env()
  > example("ggplot2_extract_legend", local = e, ask = FALSE)
  
  ggp2__> # a simple plot
  ggp2__> my_plot <-
  ggp2__+   ggplot2::ggplot(mtcars) +
  ggp2__+   ggplot2::aes(x = wt, y = mpg, color = wt, shape = factor(cyl)) +
  ggp2__+   ggplot2::geom_point()
  
  ggp2__> my_plot
  
  ggp2__> # extract the legend.  the return object is a list with two elements, the first
  ggp2__> # element is the legend, the second is the original plot sans legend.
  ggp2__> temp <- ggplot2_extract_legend(my_plot)
  
  ggp2__> # view just the legend.  This can be done via a call to the object or using
  ggp2__> # plot or print.
  ggp2__> temp
  
  ggp2__> plot(temp[[1]])
  
  ggp2__> # the original plot without the legened
  ggp2__> plot(temp[[2]])
  > ls(envir = e)
  [1] "my_plot" "temp"   
  > 
  > stopifnot(identical(names(e$temp), c("legend", "plot")))
  > 
  > ################################################################################
  > e_qacf <- new.env()
  > example("qacf", local = e_qacf, ask = FALSE)
  
  qacf> # Generate a random data set
  qacf> set.seed(42)
  
  qacf> n <- 250
  
  qacf> x1 <- x2 <- x3 <- x4 <- vector('numeric', length = n)
  
  qacf> x1[1] <- runif(1)
  
  qacf> x2[1] <- runif(1)
  
  qacf> x3[1] <- runif(1)
  
  qacf> x4[1] <- runif(1)
  
  qacf> # white noise
  qacf> Z_1 <- rnorm(n, 0, 1)
  
  qacf> Z_2 <- rnorm(n, 0, 2)
  
  qacf> Z_3 <- rnorm(n, 0, 5)
  
  qacf> for(i in 2:n)
  qacf+ {
  qacf+   x1[i] <- x1[i-1] + Z_1[i] - Z_1[i-1] + x4[i-1] - x2[i-1]
  qacf+   x2[i] <- x2[i-1] - 2 * Z_2[i] + Z_2[i-1] - x4[i-1]
  qacf+   x3[i] <- x3[i-1] + x2[i-1] + 0.2 * Z_3[i] + Z_3[i-1]
  qacf+   x4[i] <- x4[i-1] + runif(1, 0.5, 1.5) * x4[i-1]
  qacf+ }
  
  qacf> testdf <- data.frame(x1, x2, x3, x4)
  
  qacf> # qacf plot for one variable
  qacf> qacf(testdf$x1)
  
  qacf> qacf(testdf$x1, show_sig = TRUE)
  
  qacf> # more than one variable
  qacf> qacf(testdf)
  
  qacf> qacf(testdf, show_sig = TRUE)
  > 
  > ################################################################################
  > e_qroc <- new.env()
  > example("qroc", local = e_qroc, ask = FALSE)
  
  qroc> #########################################################
  qroc> # Example 1
  qroc> 
  qroc> df <-
  qroc+   data.frame(
  qroc+       truth = c(1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0)
  qroc+     , pred  = c(1, 1, 1, 1, 1, 1, 0, 0, 1, 0, 0, 0)
  qroc+   )
  
  qroc> cm <- confusion_matrix(df$truth, df$pred)
  
  qroc> qroc(cm)
  
  qroc> qprc(cm)
  
  qroc> #########################################################
  qroc> # Getting a ROC or PRC plot from a glm object:
  qroc> 
  qroc> mod <- glm(
  qroc+   formula = spam ~ word_freq_our + word_freq_over + capital_run_length_total
  qroc+ , data = spambase
  qroc+ , family = binomial()
  qroc+ )
  
  qroc> qroc(mod)
  
  qroc> qprc(mod)
  
  qroc> #########################################################
  qroc> # View the vignette for more examples
  qroc> ## Not run: 
  qroc> ##D vignette("qwraps2-graphics")
  qroc> ## End(Not run)
  qroc> 
  qroc> 
  qroc> 
  qroc> 
  > 
  > ################################################################################
  > e_qkmp <- new.env()
  > example("qkmplot", local = e_qkmp, ask = FALSE)
  
  qkmplt> require(survival)
  Loading required package: survival
  
  qkmplt> leukemia.surv <- survival::survfit(survival::Surv(time, status) ~ x, data = survival::aml)
  Error in loadNamespace(x) : there is no package called 'survival'
  Calls: example ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'survival'
  Execution halted
Running the tests in ‘tests/test-summary_table.R’ failed.
Complete output:
  > library(qwraps2)
  > qs <- qsummary(mtcars2[c("cyl", "cyl_factor", "cyl_character")])
  > 
  > stopifnot(identical(qs[["cyl"]],
  +                     list("minimum"      = ~ qwraps2::frmt(min(cyl)),
  +                          "median (IQR)" = ~ qwraps2::median_iqr(cyl),
  +                          "mean (sd)"    = ~ qwraps2::mean_sd(cyl),
  +                          "maximum"      = ~ qwraps2::frmt(max(cyl)))))
  > 
  > stopifnot(identical(qs[["cyl_factor"]],
  +                   list("6 cylinders" = ~ qwraps2::n_perc(cyl_factor == "6 cylinders", digits = 0, show_symbol = FALSE),
  +                        "4 cylinders" = ~ qwraps2::n_perc(cyl_factor == "4 cylinders", digits = 0, show_symbol = FALSE),
  +                        "8 cylinders" = ~ qwraps2::n_perc(cyl_factor == "8 cylinders", digits = 0, show_symbol = FALSE))))
  > 
  > stopifnot(identical(qs[["cyl_character"]],
  +                   list("4 cylinders" = ~ qwraps2::n_perc(cyl_character == "4 cylinders", digits = 0, show_symbol = FALSE),
  +                        "6 cylinders" = ~ qwraps2::n_perc(cyl_character == "6 cylinders", digits = 0, show_symbol = FALSE),
  +                        "8 cylinders" = ~ qwraps2::n_perc(cyl_character == "8 cylinders", digits = 0, show_symbol = FALSE))))
  > 
  > # expect warnings
  > temp <- dplyr::group_by(mtcars, am, vs)
  Error in loadNamespace(x) : there is no package called 'dplyr'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  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
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 ERRORs
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/qwraps2.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:57.32, 119.67 + 12.12