Last updated on 2026-06-07 20:52:00 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.6.16 | 29.31 | 734.07 | 763.38 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.6.16 | 18.53 | 415.94 | 434.47 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.6.16 | 48.00 | 1186.04 | 1234.04 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.6.16 | 50.00 | 1195.61 | 1245.61 | OK | |
| r-devel-windows-x86_64 | 0.6.16 | 31.00 | 651.00 | 682.00 | OK | |
| r-patched-linux-x86_64 | 0.6.16 | 30.79 | 696.13 | 726.92 | OK | |
| r-release-linux-x86_64 | 0.6.16 | 24.15 | 699.62 | 723.77 | OK | |
| r-release-macos-arm64 | 0.6.16 | 6.00 | 162.00 | 168.00 | OK | |
| r-release-macos-x86_64 | 0.6.16 | 19.00 | 693.00 | 712.00 | OK | |
| r-release-windows-x86_64 | 0.6.16 | 29.00 | 652.00 | 681.00 | OK | |
| r-oldrel-macos-arm64 | 0.6.16 | 6.00 | 158.00 | 164.00 | OK | |
| r-oldrel-macos-x86_64 | 0.6.16 | 21.00 | 926.00 | 947.00 | OK | |
| r-oldrel-windows-x86_64 | 0.6.16 | 42.00 | 887.00 | 929.00 | OK |
Version: 0.6.16
Check: examples
Result: ERROR
Running examples in ‘rtables-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: custom_split_funs
> ### Title: Custom split functions
> ### Aliases: custom_split_funs
>
> ### ** Examples
>
> # Example of a picky split function. The number of values in the column variable
> # var decrees if we are going to print also the column with all observation
> # or not.
>
> picky_splitter <- function(var) {
+ # Main layout function
+ function(df, spl, vals, labels, trim) {
+ orig_vals <- vals
+
+ # Check for number of levels if all are selected
+ if (is.null(vals)) {
+ vec <- df[[var]]
+ vals <- unique(vec)
+ }
+
+ # Do a split with or without All obs
+ if (length(vals) == 1) {
+ do_base_split(spl = spl, df = df, vals = vals, labels = labels, trim = trim)
+ } else {
+ fnc_tmp <- add_overall_level("Overall", label = "All Obs", first = FALSE)
+ fnc_tmp(df = df, spl = spl, vals = orig_vals, trim = trim)
+ }
+ }
+ }
>
> # Data sub-set
> d1 <- subset(ex_adsl, ARM == "A: Drug X" | (ARM == "B: Placebo" & SEX == "F"))
> d1 <- subset(d1, SEX %in% c("M", "F"))
> d1$SEX <- factor(d1$SEX)
>
> # This table uses the number of values in the SEX column to add the overall col or not
> lyt <- basic_table() %>%
+ split_cols_by("ARM", split_fun = drop_split_levels) %>%
+ split_cols_by("SEX", split_fun = picky_splitter("SEX")) %>%
+ analyze("AGE", show_labels = "visible")
> tbl <- build_table(lyt, d1)
> tbl
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'toString': cannot open file '/tmp/RtmpShXy2t/file1d7891795481e2.pdf'
Calls: <Anonymous> ... matrix_form -> open_font_dev -> pdf -> .handleSimpleError -> h
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.6.16
Check: tests
Result: ERROR
Running ‘testthat.R’ [166s/181s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> if (requireNamespace("testthat", quietly = TRUE)) {
+ library(testthat)
+ library(rtables)
+ test_check("rtables", reporter = "check")
+ }
Loading required package: formatters
Attaching package: 'formatters'
The following object is masked from 'package:base':
%||%
Loading required package: magrittr
Attaching package: 'magrittr'
The following objects are masked from 'package:testthat':
equals, is_less_than, not
Attaching package: 'rtables'
The following object is masked from 'package:utils':
str
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
Saving _problems/test-default_split_funs-41.R
Saving _problems/test-printing-252.R
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 1852 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-default_split_funs.R:35:3'): keep_split_levels(reorder) works correctly ──
Error in `file(file, if (append) "a" else "w")`: cannot open the connection
Backtrace:
▆
1. └─testthat::expect_silent(...) at test-default_split_funs.R:35:3
2. └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. └─testthat (local) .capture(...)
4. └─withr::with_output_sink(...)
5. └─withr:::set_output_sink(file = new, append = append, split = split)
6. └─withr:::output_sink(file = file, append = append, split = split)
7. └─base::sink(file = file, append = append, type = "output", split = split)
8. └─base::file(file, if (append) "a" else "w")
── Error ('test-printing.R:252:3'): alignment works ────────────────────────────
Error in `pdf(tmppdf)`: cannot open file '/tmp/RtmpO3rB5j/file1da6206240d4d2.pdf'
Backtrace:
▆
1. ├─base::toString(aligntab) at test-printing.R:252:3
2. └─rtables::toString(aligntab)
3. └─rtables (local) .local(x, ...)
4. ├─base::toString(...)
5. └─formatters::toString(...)
6. └─formatters (local) .local(x, ...)
7. └─formatters::open_font_dev(fontspec)
8. └─grDevices::pdf(tmppdf)
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 1852 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.6.16
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘advanced_usage.Rmd’ using rmarkdown
--- finished re-building ‘advanced_usage.Rmd’
--- re-building ‘ard_how_to.Rmd’ using rmarkdown
--- finished re-building ‘ard_how_to.Rmd’
--- re-building ‘baseline.Rmd’ using rmarkdown
--- finished re-building ‘baseline.Rmd’
--- re-building ‘clinical_trials.Rmd’ using rmarkdown
--- finished re-building ‘clinical_trials.Rmd’
--- re-building ‘col_counts.Rmd’ using rmarkdown
Warning in file("", "w+b") :
cannot open file '/tmp/RtmpqAeHt2/Rf2030ef79b0d135': No space left on device
Quitting from col_counts.Rmd:67-70 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cannot open the connection
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Quitting from col_counts.Rmd:67-70 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
file("", "w+b")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'col_counts.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘col_counts.Rmd’
--- re-building ‘custom_appearance.Rmd’ using rmarkdown
--- finished re-building ‘custom_appearance.Rmd’
--- re-building ‘example_analysis_coxreg.Rmd’ using rmarkdown
Quitting from example_analysis_coxreg.Rmd:389-392 [unnamed-chunk-11]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error in content (summary) function: there is no package called 'car'
occured at path: root
---
Backtrace:
▆
1. └─rtables::build_table(lyt, anl)
2. └─rtables:::.make_ctab(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'example_analysis_coxreg.Rmd' failed with diagnostics:
Error in content (summary) function: there is no package called 'car'
occured at path: root
--- failed re-building ‘example_analysis_coxreg.Rmd’
--- re-building ‘exploratory_analysis.Rmd’ using rmarkdown
--- finished re-building ‘exploratory_analysis.Rmd’
--- re-building ‘format_precedence.Rmd’ using rmarkdown
--- finished re-building ‘format_precedence.Rmd’
--- re-building ‘guided_intermediate.Rmd’ using rmarkdown
--- finished re-building ‘guided_intermediate.Rmd’
--- re-building ‘guided_intermediate_afun_reqs.Rmd’ using rmarkdown
--- finished re-building ‘guided_intermediate_afun_reqs.Rmd’
--- re-building ‘guided_intermediate_split_reqs.Rmd’ using rmarkdown
--- finished re-building ‘guided_intermediate_split_reqs.Rmd’
--- re-building ‘guided_intermediate_translating_shells.Rmd’ using rmarkdown
--- finished re-building ‘guided_intermediate_translating_shells.Rmd’
--- re-building ‘introspecting_tables.Rmd’ using rmarkdown
Quitting from introspecting_tables.Rmd:142-144 [unnamed-chunk-16]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `pdf()`:
! cannot open file '/tmp/RtmpIw6q22/file20e45e6f458acd.pdf'
---
Backtrace:
▆
1. └─rtables::col_paths_summary(tbl)
2. └─rtables:::mat_as_string(mat)
3. └─base::apply(...)
4. └─rtables (local) FUN(newX[, i], ...)
5. ├─base::paste(unlist(mapply(padstr, row, colwidths, "left")), collapse = colsep)
6. ├─base::unlist(mapply(padstr, row, colwidths, "left"))
7. └─base::mapply(padstr, row, colwidths, "left")
8. └─formatters (local) `<fn>`(dots[[1L]][[2L]], dots[[2L]][[2L]], dots[[3L]][[1L]])
9. └─formatters::nchar_ttype(x, fontspec)
10. └─formatters::open_font_dev(fontspec)
11. └─grDevices::pdf(tmppdf)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'introspecting_tables.Rmd' failed with diagnostics:
cannot open file '/tmp/RtmpIw6q22/file20e45e6f458acd.pdf'
--- failed re-building ‘introspecting_tables.Rmd’
--- re-building ‘manual_table_construction.Rmd’ using rmarkdown
--- finished re-building ‘manual_table_construction.Rmd’
--- re-building ‘pathing.Rmd’ using rmarkdown
--- finished re-building ‘pathing.Rmd’
--- re-building ‘rtables.Rmd’ using rmarkdown
Warning in file("", "w+b") :
cannot open file '/tmp/RtmprzY94f/Rf2110b644955ecd': No space left on device
Quitting from rtables.Rmd:52-55 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cannot open the connection
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Quitting from rtables.Rmd:52-55 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
file("", "w+b")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'rtables.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rtables.Rmd’
--- re-building ‘sorting_pruning.Rmd’ using rmarkdown
--- finished re-building ‘sorting_pruning.Rmd’
--- re-building ‘split_functions.Rmd’ using rmarkdown
--- finished re-building ‘split_functions.Rmd’
--- re-building ‘subsetting_tables.Rmd’ using rmarkdown
--- finished re-building ‘subsetting_tables.Rmd’
--- re-building ‘tabulation_concepts.Rmd’ using rmarkdown
--- finished re-building ‘tabulation_concepts.Rmd’
--- re-building ‘tabulation_dplyr.Rmd’ using rmarkdown
--- finished re-building ‘tabulation_dplyr.Rmd’
--- re-building ‘title_footer.Rmd’ using rmarkdown
--- finished re-building ‘title_footer.Rmd’
SUMMARY: processing the following files failed:
‘col_counts.Rmd’ ‘example_analysis_coxreg.Rmd’
‘introspecting_tables.Rmd’ ‘rtables.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc