- using R Under development (unstable) (2025-12-11 r89150)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
- running under: Fedora Linux 42 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘tern.gee/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘tern.gee’ version ‘0.1.5’
- 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 ‘tern.gee’ can be installed ... [23s/42s] OK
See the install log for details.
- 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 ... [7s/12s] 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 ... [26s/42s] 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 installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [10s/17s] ERROR
Running examples in ‘tern.gee-Ex.R’ failed
The error most likely occurred in:
> ### Name: tabulate_gee
> ### Title: Tabulation of a GEE Model
> ### Aliases: tabulate_gee as.rtable.tern_gee s_lsmeans_logistic
> ### a_lsmeans_logistic summarize_gee_logistic
>
> ### ** Examples
>
> library(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
>
> df <- fev_data %>%
+ mutate(AVAL = as.integer(fev_data$FEV1 > 30))
> df_counts <- df %>%
+ select(USUBJID, ARMCD) %>%
+ unique()
>
> lsmeans_df <- lsmeans(fit_gee(vars = vars_gee(arm = "ARMCD"), data = df))
>
> s_lsmeans_logistic(lsmeans_df[1, ], .in_ref_col = TRUE)
$n
[1] 420
$adj_prop_se
[1] 0.88390403 0.01948562
$adj_prop_ci
[1] 0.8398239 0.9170515
attr(,"label")
[1] "95% CI"
$odds_ratio_est
character(0)
$odds_ratio_ci
character(0)
attr(,"label")
[1] "95% CI"
$log_odds_ratio_est
character(0)
$log_odds_ratio_ci
character(0)
attr(,"label")
[1] "95% CI"
>
> s_lsmeans_logistic(lsmeans_df[2, ], .in_ref_col = FALSE)
$n
[1] 380
$adj_prop_se
[1] 0.94325891 0.01386798
$adj_prop_ci
[1] 0.9090296 0.9651032
attr(,"label")
[1] "95% CI"
$odds_ratio_est
[1] 2.18346
$odds_ratio_ci
[1] 1.161678 4.103974
attr(,"label")
[1] "95% CI"
$log_odds_ratio_est
[1] 0.7809108
$log_odds_ratio_ci
[1] 0.1498659 1.4119557
attr(,"label")
[1] "95% CI"
> basic_table() %>%
+ split_cols_by("ARMCD") %>%
+ add_colcounts() %>%
+ summarize_gee_logistic(
+ .in_ref_col = FALSE
+ ) %>%
+ build_table(lsmeans_df, alt_counts_df = df_counts)
Error in match.arg(round_type) : 'arg' must be of length 1
Calls: %>% ... <Anonymous> -> format_rcell -> format_value -> match.arg
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [15s/26s] ERROR
Running ‘testthat.R’ [15s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> pkg_name <- "tern.gee"
> library(pkg_name, character.only = TRUE)
Loading required package: tern
Loading required package: rtables
Loading required package: formatters
Attaching package: 'formatters'
The following object is masked from 'package:base':
%||%
Loading required package: magrittr
Attaching package: 'rtables'
The following object is masked from 'package:utils':
str
> testthat::test_check(pkg_name)
Attaching package: 'testthat'
The following objects are masked from 'package:magrittr':
equals, is_less_than, not
Saving _problems/test-tabulate_gee-32.R
Saving _problems/test-tabulate_gee-71.R
Saving _problems/test-tabulate_gee-96.R
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-tabulate_gee.R:32:3'): h_gee_cov works as expected ─────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'toString': 'arg' must be of length 1
Backtrace:
▆
1. ├─testthat::expect_snapshot(result) at test-tabulate_gee.R:32:3
2. │ └─testthat:::expect_snapshot_(...)
3. │ ├─testthat:::with_is_snapshotting(...)
4. │ └─testthat:::verify_exec(quo_get_expr(x), quo_get_env(x), replay)
5. │ └─evaluate::evaluate(source, envir = env, new_device = FALSE, output_handler = handler)
6. │ ├─base::withRestarts(...)
7. │ │ └─base (local) withRestartList(expr, restarts)
8. │ │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
9. │ │ │ └─base (local) doWithOneRestart(return(expr), restart)
10. │ │ └─base (local) withRestartList(expr, restarts[-nr])
11. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
12. │ │ └─base (local) doWithOneRestart(return(expr), restart)
13. │ ├─evaluate:::with_handlers(...)
14. │ │ ├─base::eval(call)
15. │ │ │ └─base::eval(call)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─watcher$print_value(ev$value, ev$visible, envir)
18. │ ├─base::withVisible(handle_value(handler, value, visible, envir))
19. │ └─evaluate:::handle_value(handler, value, visible, envir)
20. │ ├─handler$value(value)
21. │ └─testthat:::testthat_print.default(value)
22. │ ├─base::print(x)
23. │ └─base::print.default(x)
24. │ ├─methods (local) `<stndrdGn>`(`<ElmntryT[,4]>`)
25. │ └─rtables (local) `<stndrdGn>`(`<ElmntryT[,4]>`)
26. │ ├─base::cat(toString(object))
27. │ ├─base::toString(object)
28. │ └─rtables::toString(object)
29. │ └─rtables (local) .local(x, ...)
30. │ ├─base::toString(...)
31. │ ├─formatters::matrix_form(...)
32. │ └─rtables::matrix_form(...)
33. │ └─rtables:::.tbl_header_mat(obj)
34. │ ├─base::matrix(...)
35. │ └─base::rapply(...)
36. │ └─rtables (local) `<fn>`(X, ...)
37. │ ├─rtables::get_formatted_cells(x)
38. │ └─rtables::get_formatted_cells(x)
39. │ ├─base::matrix(...)
40. │ ├─base::unlist(...)
41. │ └─base::Map(...)
42. │ └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
43. │ └─rtables (local) `<fn>`(val = dots[[1L]][[1L]], spn = dots[[2L]][[1L]], shelli = dots[[3L]][[1L]])
44. │ └─rtables::format_rcell(...)
45. │ └─formatters::format_value(...)
46. │ └─base::match.arg(round_type)
47. │ └─base::stop(gettextf("'%s' must be of length 1", "arg"), domain = NA)
48. └─base::.handleSimpleError(...)
49. └─base (local) h(simpleError(msg, call))
── Error ('test-tabulate_gee.R:64:3'): summarize_gee_logistic works as expected with covariates in the model ──
Error in `match.arg(round_type)`: 'arg' must be of length 1
Backtrace:
▆
1. ├─... %>% ... at test-tabulate_gee.R:64:3
2. └─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl)
3. └─rtables::update_ref_indexing(tab)
4. ├─formatters::make_row_df(tt)
5. └─rtables::make_row_df(tt)
6. └─rtables (local) .local(...)
7. ├─formatters::make_row_df(...)
8. └─rtables::make_row_df(...)
9. └─rtables (local) .local(...)
10. ├─formatters::pagdfrow(...)
11. │ └─base::data.frame(...)
12. ├─formatters::nlines(...)
13. └─rtables::nlines(...)
14. ├─base::as.vector(get_formatted_cells(x))
15. ├─rtables::get_formatted_cells(x)
16. └─rtables::get_formatted_cells(x)
17. ├─base::matrix(...)
18. ├─base::unlist(...)
19. └─base::Map(...)
20. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
21. └─rtables (local) `<fn>`(val = dots[[1L]][[1L]], spn = dots[[2L]][[1L]], shelli = dots[[3L]][[1L]])
22. └─rtables::format_rcell(...)
23. └─formatters::format_value(...)
24. └─base::match.arg(round_type)
── Error ('test-tabulate_gee.R:89:3'): summarize_gee_logistic works as expected with no covariates in the model ──
Error in `match.arg(round_type)`: 'arg' must be of length 1
Backtrace:
▆
1. ├─... %>% ... at test-tabulate_gee.R:89:3
2. └─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl)
3. └─rtables::update_ref_indexing(tab)
4. ├─formatters::make_row_df(tt)
5. └─rtables::make_row_df(tt)
6. └─rtables (local) .local(...)
7. ├─formatters::make_row_df(...)
8. └─rtables::make_row_df(...)
9. └─rtables (local) .local(...)
10. ├─formatters::pagdfrow(...)
11. │ └─base::data.frame(...)
12. ├─formatters::nlines(...)
13. └─rtables::nlines(...)
14. ├─base::as.vector(get_formatted_cells(x))
15. ├─rtables::get_formatted_cells(x)
16. └─rtables::get_formatted_cells(x)
17. ├─base::matrix(...)
18. ├─base::unlist(...)
19. └─base::Map(...)
20. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
21. └─rtables (local) `<fn>`(val = dots[[1L]][[1L]], spn = dots[[2L]][[1L]], shelli = dots[[3L]][[1L]])
22. └─rtables::format_rcell(...)
23. └─formatters::format_value(...)
24. └─base::match.arg(round_type)
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ]
Error:
! Test failures.
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [22s/38s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘tern-gee.Rmd’ using rmarkdown
Quitting from tern-gee.Rmd:122-133 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `match.arg()`:
! 'arg' must be of length 1
---
Backtrace:
▆
1. ├─... %>% build_table(fev_lsmeans, alt_counts_df = fev_counts)
2. └─rtables::build_table(., fev_lsmeans, alt_counts_df = fev_counts)
3. └─rtables::update_ref_indexing(tab)
4. ├─formatters::make_row_df(tt)
5. └─rtables::make_row_df(tt)
6. └─rtables (local) .local(...)
7. ├─formatters::make_row_df(...)
8. └─rtables::make_row_df(...)
9. └─rtables (local) .local(...)
10. ├─formatters::pagdfrow(...)
11. │ └─base::data.frame(...)
12. ├─formatters::nlines(...)
13. └─rtables::nlines(...)
14. ├─base::as.vector(get_formatted_cells(x))
15. ├─rtables::get_formatted_cells(x)
16. └─rtables::get_formatted_cells(x)
17. ├─base::matrix(...)
18. ├─base::unlist(...)
19. └─base::Map(...)
20. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
21. └─rtables (local) `<fn>`(val = dots[[1L]][[1L]], spn = dots[[2L]][[1L]], shelli = dots[[3L]][[1L]])
22. └─rtables::format_rcell(...)
23. └─formatters::format_value(...)
24. └─base::match.arg(round_type)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'tern-gee.Rmd' failed with diagnostics:
'arg' must be of length 1
--- failed re-building ‘tern-gee.Rmd’
SUMMARY: processing the following file failed:
‘tern-gee.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [6s/12s] 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: 3 ERRORs