Fix deprecated dplyr functions in vignette

[Copilot]

Vignette rebuild fails on deprecated dplyr functions that are now defunct.

Changes

• vignettes/zibr.Rmd: Replace 4 instances of add_rownames() with rownames_to_column()
  • Lines 175, 182: Data joins with sample.info
  • Lines 250, 257: P-value adjustment for ZIBR and LME results
• vignettes/zibr.Rmd: Replace 2 instances of mutate_each(funs()) with mutate(across())
  • Lines 250, 257: Changed mutate_each(funs(p.adjust(., "fdr")), -Species) to mutate(across(-Species, ~p.adjust(., "fdr")))
• vignettes/zibr.Rmd: Add library(tibble) to setup chunk
• DESCRIPTION: Add tibble to Suggests

Deprecated Functions Fixed

• add_rownames() - deprecated in dplyr 1.0.0, replaced with tibble::rownames_to_column()
• mutate_each() and funs() - deprecated in dplyr 0.7.0, replaced with mutate() + across()

Original prompt

Version: 1.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘zibr.Rmd’ using rmarkdown

Quitting from zibr.Rmd:169-286 [unnamed-chunk-11]

<error/lifecycle_error_deprecated>
Error:
! `add_rownames()` was deprecated in dplyr 1.0.0 and is now defunct.
ℹ Please use `tibble::rownames_to_column()` instead.
---
Backtrace:
     ▆
  1. ├─... %>% as.data.frame()
  2. ├─base::as.data.frame(.)
  3. ├─dplyr::mutate(., Time.X.Treatment = Time * Treat)
  4. ├─dplyr::mutate(...)
  5. ├─dplyr::mutate(., Subject = paste("S", Subject, sep = ""))
  6. ├─dplyr::select(., Sample, Subject, Time, Response, Treat)
  7. ├─dplyr::mutate(...)
  8. ├─dplyr::left_join(...)
  9. ├─dplyr::select(., Subject)
 10. ├─dplyr::filter(., count == 4)
 11. ├─dplyr::summarise(., count = n())
 12. ├─dplyr::group_by(., Subject)
 13. ├─dplyr::select(., Sample, Time, Subject, Response, Treatment.Specific)
 14. ├─dplyr::filter(., Treatment.Specific != "PEN")
 15. ├─dplyr::left_join(...)
 16. ├─dplyr:::left_join.data.frame(...)
 17. │ └─dplyr::auto_copy(x, y, copy = copy)
 18. │   ├─dplyr::same_src(x, y)
 19. │   └─dplyr:::same_src.data.frame(x, y)
 20. │     └─base::is.data.frame(y)
 21. └─dplyr::add_rownames(sample.info, var = "Sample")
 22.   └─lifecycle::deprecate_stop("1.0.0", "add_rownames()", "tibble::rownames_to_column()")
 23.     └─lifecycle:::deprecate_stop0(msg)

Error: processing vignette 'zibr.Rmd' failed with diagnostics:
add_rownames() was deprecated in dplyr 1.0.0 and is now defunct.
ℹ Please use tibble::rownames_to_column() instead.
--- failed re-building ‘zibr.Rmd’

SUMMARY: processing the following file failed:
‘zibr.Rmd’

Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘zibr.Rmd’ using rmarkdown

Quitting from zibr.Rmd:169-286 [unnamed-chunk-11]

<error/lifecycle_error_deprecated>
Error:
! `add_rownames()` was deprecated in dplyr 1.0.0 and is now defunct.
ℹ Please use `tibble::rownames_to_column()` instead.
---
Backtrace:
     ▆
  1. ├─... %>% as.data.frame()
  2. ├─base::as.data.frame(.)
  3. ├─dplyr::mutate(., Time.X.Treatment = Time * Treat)
  4. ├─dplyr::mutate(...)
  5. ├─dplyr::mutate(., Subject = paste("S", Subject, sep = ""))
  6. ├─dplyr::select(., Sample, Subject, Time, Response, Treat)
  7. ├─dplyr::mutate(...)
  8. ├─dplyr::left_join(...)
  9. ├─dplyr::select(., Subject)
 10. ├─dplyr::filter(., count == 4)
 11. ├─dplyr::summarise(., count = n())
 12. ├─dplyr::group_by(., Subject)
 13. ├─dplyr::select(., Sample, Time, Subject, Response, Treatment.Specific)
 14. ├─dplyr::filter(., Treatment.Specific != "PEN")
 15. ├─dplyr::left_join(...)
 16. ├─dplyr:::left_join.data.frame(...)
 17. │ └─dplyr::auto_copy(x, y, copy = copy)
 18. │   ├─dplyr::same_src(x, y)
 19. │   └─dplyr:::same_src.data.frame(x, y)
 20. │     └─base::is.data.frame(y)
 21. └─dplyr::add_rownames(sample.info, var = "Sample")
 22.   └─lifecycle::deprecate_stop("1.0.0", "add_rownames()", "tibble::rownames_to_column()")
 23.     └─lifecycle:::deprecate_stop0(msg)

Error: processing vignette 'zibr.Rmd' failed with diagnostics:
add_rownames() was deprecated in dplyr 1.0.0 and is now defunct.
ℹ Please use tibble::rownames_to_column() instead.
--- failed re-building ‘zibr.Rmd’

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[Ulthran]

@copilot Tests need to pass. Make sure you can build the vignettes without error before committing.

[Copilot]

@copilot Tests need to pass. Make sure you can build the vignettes without error before committing.

Fixed both deprecated dplyr functions causing vignette build failures:

1. Commit 295b6c5: Replaced add_rownames() with rownames_to_column() (4 instances)
2. Commit 7ec0ac1: Replaced mutate_each(funs()) with mutate(across()) (2 instances)

The vignettes should now build without errors. The CI workflows are awaiting approval to run.

[Copilot]

Pull request overview

This pull request fixes a build failure caused by deprecated dplyr functions that are now defunct in newer versions of dplyr. The vignette was failing to rebuild because it used add_rownames(), mutate_each(), and funs(), which were deprecated in dplyr 1.0.0 and 0.7.0 respectively.

Changes:

• Replaced add_rownames() with tibble::rownames_to_column() in 4 locations
• Replaced mutate_each(funs()) with mutate(across()) in 2 locations
• Added library(tibble) to vignette setup and tibble to DESCRIPTION Suggests

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File	Description
vignettes/zibr.Rmd	Updated deprecated dplyr functions to modern equivalents and added tibble library import
DESCRIPTION	Added tibble package to Suggests field for vignette dependency

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