CRAN Package Check Results for Maintainer ‘Andrew Jackson <jacksoan at tcd.ie>’

Last updated on 2026-02-04 04:50:41 CET.

Package	ERROR	OK
SIBER	3	10

Package SIBER

Current CRAN status: ERROR: 3, OK: 10

Version: 2.1.9
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘Centroid-Vectors.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Centroid-Vectors.Rmd’ --- re-building ‘Customising-Plots-Manually.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Customising-Plots-Manually.Rmd’ --- re-building ‘Ellipse-Overlap.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Ellipse-Overlap.Rmd’ --- re-building ‘Introduction-to-SIBER.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Introduction-to-SIBER.Rmd’ --- re-building ‘Plot-SIA-ggplot2.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Plot-SIA-ggplot2.Rmd’ --- re-building ‘Plot-posterior-ellipses.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Plot-posterior-ellipses.Rmd’ --- re-building ‘Points-Inside-Outside-Ellipse.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Points-Inside-Outside-Ellipse.Rmd’ --- re-building ‘Test-convergence.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Test-convergence.Rmd’ --- re-building ‘kapow-example.Rmd’ using rmarkdown Quitting from kapow-example.Rmd:90-131 [make-packs] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/purrr_error_indexed> Error in `purrr::map()`: ℹ In index: 1. ℹ With name: 11. Caused by error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help --- Backtrace: ▆ 1. ├─purrr::map(...) 2. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 3. │ ├─purrr:::with_indexed_errors(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ ├─purrr:::call_with_cleanup(...) 6. │ └─SIBER (local) .f(.x[[i]], ...) 7. │ └─... %>% do(calcBoundaries(.data)) 8. ├─dplyr::do(., calcBoundaries(.data)) 9. └─dplyr::group_by_(., .dots = group) 10. └─dplyr:::lazy_defunct("group_by") 11. └─lifecycle::deprecate_stop(...) 12. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'kapow-example.Rmd' failed with diagnostics: ℹ In index: 1. ℹ With name: 11. Caused by error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help --- failed re-building ‘kapow-example.Rmd’ --- re-building ‘siber-comparing-communities.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘siber-comparing-communities.Rmd’ --- re-building ‘siber-comparing-populations.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘siber-comparing-populations.Rmd’ SUMMARY: processing the following file failed: ‘kapow-example.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.1.9
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘Centroid-Vectors.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Centroid-Vectors.Rmd’ --- re-building ‘Customising-Plots-Manually.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Customising-Plots-Manually.Rmd’ --- re-building ‘Ellipse-Overlap.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Ellipse-Overlap.Rmd’ --- re-building ‘Introduction-to-SIBER.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Introduction-to-SIBER.Rmd’ --- re-building ‘Plot-SIA-ggplot2.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Plot-SIA-ggplot2.Rmd’ --- re-building ‘Plot-posterior-ellipses.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Plot-posterior-ellipses.Rmd’ --- re-building ‘Points-Inside-Outside-Ellipse.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Points-Inside-Outside-Ellipse.Rmd’ --- re-building ‘Test-convergence.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Test-convergence.Rmd’ --- re-building ‘kapow-example.Rmd’ using rmarkdown Quitting from kapow-example.Rmd:90-131 [make-packs] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/purrr_error_indexed> Error in `purrr::map()`: ℹ In index: 1. ℹ With name: 11. Caused by error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help --- Backtrace: ▆ 1. ├─purrr::map(...) 2. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 3. │ ├─purrr:::with_indexed_errors(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ ├─purrr:::call_with_cleanup(...) 6. │ └─SIBER (local) .f(.x[[i]], ...) 7. │ └─... %>% do(calcBoundaries(.data)) 8. ├─dplyr::do(., calcBoundaries(.data)) 9. └─dplyr::group_by_(., .dots = group) 10. └─dplyr:::lazy_defunct("group_by") 11. └─lifecycle::deprecate_stop(...) 12. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'kapow-example.Rmd' failed with diagnostics: ℹ In index: 1. ℹ With name: 11. Caused by error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help --- failed re-building ‘kapow-example.Rmd’ --- re-building ‘siber-comparing-communities.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘siber-comparing-communities.Rmd’ --- re-building ‘siber-comparing-populations.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘siber-comparing-populations.Rmd’ SUMMARY: processing the following file failed: ‘kapow-example.Rmd’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc