• using R Under development (unstable) (2024-10-01 r87205)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.0 (4)     Debian flang-new version 19.1.0 (4)
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘pubh/DESCRIPTION’ ... OK
• this is package ‘pubh’ version ‘1.3.7’
• 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 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 ‘pubh’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [5s/7s] OK
• checking whether the package can be loaded with stated dependencies ... [5s/6s] OK
• checking whether the package can be unloaded cleanly ... [5s/6s] OK
• checking whether the namespace can be loaded with stated dependencies ... [5s/7s] OK
• checking whether the namespace can be unloaded cleanly ... [5s/7s] OK
• checking loading without being on the library search path ... [5s/7s] 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 ... [28s/34s] OK
• checking Rd files ... [1s/1s] 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 ... [0s/0s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [7s/9s] ERROR Running examples in ‘pubh-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: Bernard > ### Title: Survival of patients with sepsis. > ### Aliases: Bernard > ### Keywords: datasets > > ### ** Examples > > require(dplyr, quietly = TRUE) Attaching package: ‘dplyr’ The following object is masked from ‘package:huxtable’:     add_rownames The following objects are masked from ‘package:stats’:     filter, lag The following objects are masked from ‘package:base’:     intersect, setdiff, setequal, union > data(Bernard) > > Bernard |> + select(fate, treat) |> + cross_tbl(by = "fate") Error in `dplyr::mutate()`: ℹ In argument: `df_stats = list(...)`. Caused by error in `dplyr::mutate()`: ℹ In argument: `stat = map(...)`. Caused by error in `glue_data()`: ! is.environment(.envir) is not TRUE Backtrace:   1. pubh::cross_tbl(select(Bernard, fate, treat), by = "fate")  51. gtsummary:::map(...)  52. base::lapply(.x, .f, ...)  53. gtsummary (local) FUN(X[[i]], ...)  54. glue::glue(...)  55. glue::glue_data(...)  56. base::stopifnot(is.environment(.envir))  57. base::stop(simpleError(msg, call = if (p <- sys.parent(1L)) sys.call(p))) Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [30s/41s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘introduction.Rmd’ using rmarkdown Quitting from lines 134-142 [unnamed-chunk-6] (introduction.Rmd) Error: processing vignette 'introduction.Rmd' failed with diagnostics: ℹ In argument: `df_stats = list(...)`. Caused by error in `dplyr::mutate()`: ℹ In argument: `stat = map(...)`. Caused by error in `glue_data()`: ! is.environment(.envir) is not TRUE --- failed re-building ‘introduction.Rmd’ --- re-building ‘regression.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/pubh.Rcheck/vign_test/pubh/vignettes/regression_files/figure-html/unnamed-chunk-3-1.png 480x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 17644 bytes Input file size = 17746 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13737   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13737 Output IDAT size = 13737 bytes (3907 bytes decrease) Output file size = 13815 bytes (3931 bytes = 22.15% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/pubh.Rcheck/vign_test/pubh/vignettes/regression_files/figure-html/unnamed-chunk-13-1.png 480x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 19783 bytes Input file size = 19885 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14442   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14442 Output IDAT size = 14442 bytes (5341 bytes decrease) Output file size = 14520 bytes (5365 bytes = 26.98% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/pubh.Rcheck/vign_test/pubh/vignettes/regression_files/figure-html/unnamed-chunk-14-1.png 480x384 pixels, 8 bits/pixel, 232 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 7074 bytes Input file size = 7860 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6204   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6204 Output IDAT size = 6204 bytes (870 bytes decrease) Output file size = 6282 bytes (1578 bytes = 20.08% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/pubh.Rcheck/vign_test/pubh/vignettes/regression_files/figure-html/unnamed-chunk-15-1.png 480x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 19570 bytes Input file size = 19672 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14240   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14240 Output IDAT size = 14240 bytes (5330 bytes decrease) Output file size = 14318 bytes (5354 bytes = 27.22% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/pubh.Rcheck/vign_test/pubh/vignettes/regression_files/figure-html/unnamed-chunk-18-1.png 480x384 pixels, 8 bits/pixel, 243 colors in palette Input IDAT size = 5174 bytes Input file size = 5993 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4302   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4302 Output IDAT size = 4302 bytes (872 bytes decrease) Output file size = 5121 bytes (872 bytes = 14.55% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/pubh.Rcheck/vign_test/pubh/vignettes/regression_files/figure-html/unnamed-chunk-23-1.png 480x384 pixels, 8 bits/pixel, 237 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8448 bytes Input file size = 9261 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7373   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7373 Output IDAT size = 7373 bytes (1075 bytes decrease) Output file size = 7451 bytes (1810 bytes = 19.54% decrease) Quitting from lines 272-288 [unnamed-chunk-25] (regression.Rmd) Error: processing vignette 'regression.Rmd' failed with diagnostics: ℹ In argument: `tbl = switch(...)`. Caused by error in `dplyr::mutate()`: ℹ In argument: `df_stats = list(...)`. Caused by error in `dplyr::mutate()`: ℹ In argument: `stat = map(...)`. Caused by error in `glue_data()`: ! is.environment(.envir) is not TRUE --- failed re-building ‘regression.Rmd’ SUMMARY: processing the following files failed:   ‘introduction.Rmd’ ‘regression.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [8s/10s] OK
• checking HTML version of manual ... [2s/3s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs