- using R version 4.4.1 Patched (2024-07-08 r86915)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-13 (Debian 13.3.0-3) 13.3.0
GNU Fortran (Debian 13.3.0-3) 13.3.0
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘pubh/DESCRIPTION’ ... OK
- this is package ‘pubh’ version ‘1.3.2’
- 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 ... [4s/5s] OK
- checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
- checking whether the package can be unloaded cleanly ... [4s/5s] OK
- checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
- checking whether the namespace can be unloaded cleanly ... [4s/5s] OK
- checking loading without being on the library search path ... [2s/2s] 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 ... [25s/31s] 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 ... [48s/63s] ERROR
Running examples in ‘pubh-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cosm_reg
> ### Title: Cosmetics for tables of regression coefficients. Converts tables
> ### generated by 'tbl_regression' to 'huxtable' and adds some cosmetics.
> ### Aliases: cosm_reg
>
> ### ** Examples
>
> require(sjlabelled, quietly = TRUE)
Attaching package: ‘sjlabelled’
The following object is masked from ‘package:huxtable’:
set_label
The following object is masked from ‘package:ggplot2’:
as_label
>
> data(diet, package = "Epi")
> diet <- diet %>%
+ var_labels(
+ chd = "Coronary Heart Disease",
+ fibre = "Fibre intake (g/day)"
+ )
>
> model_binom <- glm(chd ~ fibre, data = diet, family = binomial)
>
> model_binom %>%
+ tbl_regression(exponentiate = TRUE) %>%
+ cosm_reg(bold = TRUE) %>%
+ theme_pubh(1) %>%
+ add_footnote(get_r2(model_binom), font_size = 9)
Error in gtsummary::modify_footnote(., everything() ~ NA, abbreviation = TRUE) :
The package "broom.helpers" (>= 1.15.0) is required.
Calls: %>% ... <Anonymous> -> tbl_regression -> check_pkg_installed
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [37s/47s] ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘introduction.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pubh.Rcheck/vign_test/pubh/vignettes/introduction_files/figure-html/unnamed-chunk-13-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 23111 bytes
Input file size = 23213 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18532
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 = 18532
Output IDAT size = 18532 bytes (4579 bytes decrease)
Output file size = 18610 bytes (4603 bytes = 19.83% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pubh.Rcheck/vign_test/pubh/vignettes/introduction_files/figure-html/unnamed-chunk-15-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 11535 bytes
Input file size = 11625 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9697
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 = 9697
Output IDAT size = 9697 bytes (1838 bytes decrease)
Output file size = 9775 bytes (1850 bytes = 15.91% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pubh.Rcheck/vign_test/pubh/vignettes/introduction_files/figure-html/unnamed-chunk-16-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 11990 bytes
Input file size = 12080 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10015
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 = 10015
Output IDAT size = 10015 bytes (1975 bytes decrease)
Output file size = 10093 bytes (1987 bytes = 16.45% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pubh.Rcheck/vign_test/pubh/vignettes/introduction_files/figure-html/unnamed-chunk-18-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 9990 bytes
Input file size = 10080 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9089
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 IDAT size = 8898
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 = 5 IDAT size = 8898
Output IDAT size = 8898 bytes (1092 bytes decrease)
Output file size = 8976 bytes (1104 bytes = 10.95% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pubh.Rcheck/vign_test/pubh/vignettes/introduction_files/figure-html/unnamed-chunk-19-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26215 bytes
Input file size = 26329 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21199
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 = 21199
Output IDAT size = 21199 bytes (5016 bytes decrease)
Output file size = 21277 bytes (5052 bytes = 19.19% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pubh.Rcheck/vign_test/pubh/vignettes/introduction_files/figure-html/unnamed-chunk-21-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 10333 bytes
Input file size = 10423 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9243
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 IDAT size = 9225
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 = 5 IDAT size = 9225
Output IDAT size = 9225 bytes (1108 bytes decrease)
Output file size = 9303 bytes (1120 bytes = 10.75% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pubh.Rcheck/vign_test/pubh/vignettes/introduction_files/figure-html/unnamed-chunk-22-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 13015 bytes
Input file size = 13105 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11089
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 = 11089
Output IDAT size = 11089 bytes (1926 bytes decrease)
Output file size = 11167 bytes (1938 bytes = 14.79% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pubh.Rcheck/vign_test/pubh/vignettes/introduction_files/figure-html/unnamed-chunk-23-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 13821 bytes
Input file size = 13911 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11838
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 = 11838
Output IDAT size = 11838 bytes (1983 bytes decrease)
Output file size = 11916 bytes (1995 bytes = 14.34% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pubh.Rcheck/vign_test/pubh/vignettes/introduction_files/figure-html/unnamed-chunk-24-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 15266 bytes
Input file size = 15356 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11891
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 = 11891
Output IDAT size = 11891 bytes (3375 bytes decrease)
Output file size = 11969 bytes (3387 bytes = 22.06% decrease)
Quitting from lines 349-353 [unnamed-chunk-26] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
The package "broom.helpers" (>= 1.15.0) is required.
--- failed re-building ‘introduction.Rmd’
--- re-building ‘regression.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/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 = 15368 bytes
Input file size = 15458 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12425
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 = 12425
Output IDAT size = 12425 bytes (2943 bytes decrease)
Output file size = 12503 bytes (2955 bytes = 19.12% decrease)
Quitting from lines 118-122 [unnamed-chunk-9] (regression.Rmd)
Error: processing vignette 'regression.Rmd' failed with diagnostics:
The package "broom.helpers" (>= 1.15.0) is required.
--- 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 ... [10s/14s] OK
- checking HTML version of manual ... [2s/4s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 ERRORs