- using R Under development (unstable) (2025-07-22 r88445)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
clang version 20.1.8
flang version 20.1.8
- running under: Fedora Linux 42 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘broom/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘broom’ version ‘1.0.8’
- 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 ‘broom’ can be installed ... [21s/26s] OK
See the install log for details.
- 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 whether startup messages can be suppressed ... 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 ... [34s/39s] 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 R/sysdata.rda ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [103s/106s] ERROR
Running examples in ‘broom-Ex.R’ failed
The error most likely occurred in:
> ### Name: tidy.epi.2by2
> ### Title: Tidy a(n) epi.2by2 object
> ### Aliases: tidy.epi.2by2 epiR_tidiers
>
> ### ** Examples
>
> ## Don't show:
> if (rlang::is_installed("epiR")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+
+ # load libraries for models and data
+ library(epiR)
+
+ # generate data
+ dat <- matrix(c(13, 2163, 5, 3349), nrow = 2, byrow = TRUE)
+
+ rownames(dat) <- c("DF+", "DF-")
+ colnames(dat) <- c("FUS+", "FUS-")
+
+ # fit model
+ fit <- epi.2by2(
+ dat = as.table(dat), method = "cross.sectional",
+ conf.level = 0.95, units = 100, outcome = "as.columns"
+ )
+
+ # summarize model fit with tidiers
+ tidy(fit, parameters = "moa")
+ tidy(fit, parameters = "stat")
+ ## Don't show:
+ }) # examplesIf
> library(epiR)
Loading required package: survival
Package epiR 2.0.85 is loaded
Type help(epi.about) for summary information
Type browseVignettes(package = 'epiR') to learn how to use epiR for applied epidemiological analyses
> dat <- matrix(c(13, 2163, 5, 3349), nrow = 2, byrow = TRUE)
> rownames(dat) <- c("DF+", "DF-")
> colnames(dat) <- c("FUS+", "FUS-")
> fit <- epi.2by2(dat = as.table(dat), method = "cross.sectional", conf.level = 0.95,
+ units = 100, outcome = "as.columns")
> tidy(fit, parameters = "moa")
Error in `dplyr::bind_rows()`:
! Can't combine `PR.strata.wald$test.statistic` <double> and `chi2.strata.fisher$test.statistic` <character>.
Backtrace:
▆
1. ├─(if (getRversion() >= "3.4") withAutoprint else force)(...)
2. │ └─base::source(...)
3. │ ├─base::withVisible(eval(ei, envir))
4. │ └─base::eval(ei, envir)
5. │ └─base::eval(ei, envir)
6. ├─generics::tidy(fit, parameters = "moa")
7. ├─broom:::tidy.epi.2by2(fit, parameters = "moa")
8. │ └─dplyr::bind_rows(massoc[names(massoc) != "chi2.correction"], .id = "term")
9. │ └─vctrs::vec_rbind(!!!dots, .names_to = .id, .error_call = current_env())
10. └─vctrs (local) `<fn>`()
11. └─vctrs::vec_default_ptype2(...)
12. ├─base::withRestarts(...)
13. │ └─base (local) withOneRestart(expr, restarts[[1L]])
14. │ └─base (local) doWithOneRestart(return(expr), restart)
15. └─vctrs::stop_incompatible_type(...)
16. └─vctrs:::stop_incompatible(...)
17. └─vctrs:::stop_vctrs(...)
18. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [36s/37s] OK
Running ‘spelling.R’
Running ‘test-all.R’ [18s/19s]
Running ‘testthat.R’ [17s/17s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [14s/14s] OK
- checking PDF version of manual ... [26s/26s] OK
- checking HTML version of manual ... [16s/16s] OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 1 ERROR