- using R Under development (unstable) (2026-09-25 r90590)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-16 (Debian 16.2.0-3) 16.2.0
GNU Fortran (Debian 16.2.0-3) 16.2.0
- running under: Debian GNU/Linux forky/sid
- using session charset: UTF-8
* current time: 2026-09-28 16:08:10 UTC
- checking for file ‘junco/DESCRIPTION’ ... OK
- this is package ‘junco’ version ‘0.1.6’
- package encoding: UTF-8
- checking CRAN incoming feasibility ... [2s/4s] OK
- 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 ‘junco’ 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 ... [3s/4s] OK
- checking whether the package can be loaded with stated dependencies ... [3s/5s] OK
- checking whether the package can be unloaded cleanly ... [3s/5s] OK
- checking whether the namespace can be loaded with stated dependencies ... [3s/4s] OK
- checking whether the namespace can be unloaded cleanly ... [4s/5s] OK
- checking loading without being on the library search path ... [4s/5s] OK
- checking whether startup messages can be suppressed ... [3s/6s] 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 ... [36s/49s] 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 installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [30s/40s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
a_freq_j 4.233 0.085 5.979
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [177s/242s] ERROR
Running ‘testthat.R’ [177s/242s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> options(rgl.useNULL = TRUE)
> library(testthat)
> library(junco)
Loading required package: formatters
Attaching package: 'formatters'
The following object is masked from 'package:base':
%||%
Loading required package: rtables
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
>
> test_check("junco")
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
Joining with `by = join_by(USUBJID)`
Joining with `by = join_by(USUBJID, ARM)`
mmrm() registered as emmeans extension
none of the combination levels appeared in the colspan treatment map; adding them automatically.
none of the combination levels appeared in the colspan treatment map; adding them automatically.
none of the combination levels appeared in the colspan treatment map; adding them automatically.
[1] 84 84 67 84
Saving _problems/test-summarize_ancova-719.R
[ FAIL 1 | WARN 0 | SKIP 25 | PASS 840 ]
══ Skipped tests (25) ══════════════════════════════════════════════════════════
• On CRAN (25): 'test-a_summarize_aval_chg_diff.R:472:1', 'test-ancova.R:4:1',
'test-docx_exporter_functions.R:9:1', 'test-estimate_proportion_diff.R:1:1',
'test-lsmeans.R:318:1', 'test-lsmeans.R:339:1', 'test-lsmeans.R:348:1',
'test-lsmeans.R:359:1', 'test-lsmeans.R:631:1', 'test-lsmeans.R:658:1',
'test-mmrm.R:81:1', 'test-mmrm.R:151:1', 'test-mmrm_rbmi.R:5:1',
'test-rbmi.R:73:3', 'test-rbmi.R:79:3', 'test-rbmi.R:120:3',
'test-rbmi.R:139:3', 'test-rbmi.R:152:3', 'test-rbmi.R:171:3',
'test-summarize_ancova.R:152:1', 'test-summarize_mmrm.R:15:1',
'test-summarize_mmrm.R:33:1', 'test-summarize_mmrm.R:70:1',
'test-tabulate_lsmeans.R:40:1', 'test-tt_to_tblfile.R:193:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-summarize_ancova.R:719:3'): a_summarize_ancova_j with multiple combined columns ──
Snapshot of code has changed:
old[5:10] vs new[5:10]
(N=86) (N=96) (N=86) (N=72) (N=182) (N=158) (N=254)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Adjusted comparison (covariates SEX)
- n 83 94 83 72 177 155 249
+ n 83 94 84 72 178 156 250
- Adjusted Mean (95% CI) -2.62 (-4.43, -0.81) -0.11 (-1.81, 1.59) -0.75 (-2.56, 1.06) -1.91 (-3.86, 0.04) -0.41 (-1.65, 0.83) -1.29 (-2.61, 0.04) -0.84 (-1.89, 0.20)
+ Adjusted Mean (95% CI) -2.64 (-4.53, -0.74) -0.11 (-1.89, 1.67) -1.90 (-3.78, -0.02) -1.89 (-3.92, 0.15) -0.95 (-2.25, 0.34) -1.89 (-3.27, -0.51) -1.22 (-2.31, -0.13)
- Difference in Adjusted Means (95% CI) 2.52 (0.03, 5.00) 1.87 (-0.69, 4.43) 0.71 (-1.95, 3.37) 2.21 (0.02, 4.41) 1.33 (-0.91, 3.58) 1.78 (-0.31, 3.87)
+ Difference in Adjusted Means (95% CI) 2.53 (-0.07, 5.12) 0.74 (-1.93, 3.41) 0.75 (-2.04, 3.53) 1.68 (-0.61, 3.97) 0.74 (-1.60, 3.09) 1.41 (-0.77, 3.60)
── Snapshots ───────────────────────────────────────────────────────────────────
To review and process snapshots locally:
* Locate check directory.
* Copy 'tests/testthat/_snaps' to local package.
* Run `testthat::snapshot_accept()` to accept all changes.
* Run `testthat::snapshot_review()` to review all changes.
[ FAIL 1 | WARN 0 | SKIP 25 | PASS 840 ]
Error:
! Test failures.
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [121s/152s] ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘ancova_combined.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘ancova_combined.Rmd’
--- re-building ‘auto_colwidths.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘auto_colwidths.Rmd’
--- re-building ‘junco.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘junco.Rmd’
--- re-building ‘standard_column_structures.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘standard_column_structures.Rmd’
--- re-building ‘table_and_listing_customizations.Rmd’ using rmarkdown
Quitting from table_and_listing_customizations.Rmd:1672-1682 [multiple_docs_table2_display]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `x[[3]]`:
! subscript out of bounds
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'table_and_listing_customizations.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘table_and_listing_customizations.Rmd’
SUMMARY: processing the following file failed:
‘table_and_listing_customizations.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [10s/13s] OK
- checking HTML version of manual ... [5s/5s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 ERRORs