Last updated on 2025-10-21 00:50:41 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| eoffice | 1 | 12 | |
| fctutils | 13 | ||
| microbial | 3 | 10 | |
| o2plsda | 8 | 5 |
Current CRAN status: NOTE: 1, OK: 12
Version: 0.2.2
Check: HTML version of manual
Result: NOTE
Found the following HTML validation problems:
col2hex.html:46:1 (col2hex.Rd:10): Warning: missing </ul> before </div>
dot-getext.html:46:1 (dot-getext.Rd:10): Warning: missing </ul> before </div>
dot-getfilename.html:46:1 (dot-getfilename.Rd:10): Warning: missing </ul> before </div>
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: OK: 13
Current CRAN status: NOTE: 3, OK: 10
Version: 0.0.22
Check: HTML version of manual
Result: NOTE
Found the following HTML validation problems:
dot-checkfile.html:46:1 (dot-checkfile.Rd:10): Warning: missing </ul> before </div>
dot-getstar.html:46:1 (dot-getstar.Rd:10): Warning: missing </ul> before </div>
dot-lda.fun.html:46:1 (dot-lda.fun.Rd:10): Warning: missing </ul> before </div>
otu_table.html:50:1 (otu_table.Rd:12): Warning: missing </ul> before </div>
phy_tree.html:51:1 (phy_tree.Rd:13): Warning: missing </ul> before </div>
psmelt.html:52:1 (psmelt.Rd:14): Warning: missing </ul> before </div>
sample_data.html:50:1 (sample_data.Rd:12): Warning: missing </ul> before </div>
subset_samples.html:52:1 (subset_samples.Rd:14): Warning: missing </ul> before </div>
subset_taxa.html:52:1 (subset_taxa.Rd:14): Warning: missing </ul> before </div>
tax_table.html:50:1 (tax_table.Rd:12): Warning: missing </ul> before </div>
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Current CRAN status: ERROR: 8, OK: 5
Version: 0.0.25
Check: examples
Result: ERROR
Running examples in ‘o2plsda-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.o2plsda
> ### Title: Score, VIP or loading plot for the O2PLS results
> ### Aliases: plot.o2plsda
>
> ### ** Examples
>
> X <- matrix(rnorm(50),10,5)
> Y <- matrix(rnorm(50),10,5)
> fit <- o2pls(X,Y,2,1,1)
> yy <- rep(c(0,1),5)
> fit0 <- oplsda(fit,yy,2)
> plot(fit0, type="score", group = factor(yy))
Error in `stat_ellipse()`:
! Problem while computing stat.
ℹ Error occurred in the 3rd layer.
Caused by error in `setup_params()`:
! The package "MASS" is required for calculating ellipses with `type =
"t"`.
Backtrace:
▆
1. ├─base (local) `<fn>`(x)
2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x)
3. │ ├─ggplot2::ggplot_build(x)
4. │ └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
5. │ └─ggplot2:::by_layer(...)
6. │ ├─rlang::try_fetch(...)
7. │ │ ├─base::tryCatch(...)
8. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
11. │ │ └─base::withCallingHandlers(...)
12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
13. │ └─l$compute_statistic(d, layout)
14. │ └─ggplot2 (local) compute_statistic(..., self = self)
15. │ └─self$stat$setup_params(data, self$stat_params)
16. │ └─ggplot2 (local) setup_params(...)
17. │ └─rlang::check_installed("MASS", "for calculating ellipses with `type = \"t\"`.")
18. │ └─base::stop(cnd)
19. └─rlang (local) `<fn>`(`<rlb_r___>`)
20. └─handlers[[1L]](cnd)
21. └─cli::cli_abort(...)
22. └─rlang::abort(...)
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.0.25
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘o2plsda.Rmd’ using knitr
Quitting from o2plsda.Rmd:91-96 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'o2plsda.Rmd' failed with diagnostics:
Problem while computing stat.
ℹ Error occurred in the 3rd layer.
Caused by error in `setup_params()`:
! The package "MASS" is required for calculating ellipses with `type =
"t"`.
--- failed re-building ‘o2plsda.Rmd’
SUMMARY: processing the following file failed:
‘o2plsda.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.0.25
Check: HTML version of manual
Result: NOTE
Found the following HTML validation problems:
dot-pls.html:63:1 (dot-pls.Rd:19): Warning: missing </ul> before </div>
loadings.o2plsda.html:55:1 (loadings.o2plsda.Rd:14): Warning: missing </ul> before </div>
loadings.plsda.html:51:1 (loadings.plsda.Rd:12): Warning: missing </ul> before </div>
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.0.25
Check: examples
Result: ERROR
Running examples in ‘o2plsda-Ex.R’ failed
The error most likely occurred in:
> ### Name: plot.o2plsda
> ### Title: Score, VIP or loading plot for the O2PLS results
> ### Aliases: plot.o2plsda
>
> ### ** Examples
>
> X <- matrix(rnorm(50),10,5)
> Y <- matrix(rnorm(50),10,5)
> fit <- o2pls(X,Y,2,1,1)
> yy <- rep(c(0,1),5)
> fit0 <- oplsda(fit,yy,2)
> plot(fit0, type="score", group = factor(yy))
Error in `stat_ellipse()`:
! Problem while computing stat.
ℹ Error occurred in the 3rd layer.
Caused by error in `setup_params()`:
! The package "MASS" is required for calculating ellipses with `type =
"t"`.
Backtrace:
▆
1. ├─base (local) `<fn>`(x)
2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x)
3. │ ├─ggplot2::ggplot_build(x)
4. │ └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
5. │ └─ggplot2:::by_layer(...)
6. │ ├─rlang::try_fetch(...)
7. │ │ ├─base::tryCatch(...)
8. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
11. │ │ └─base::withCallingHandlers(...)
12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
13. │ └─l$compute_statistic(d, layout)
14. │ └─ggplot2 (local) compute_statistic(..., self = self)
15. │ └─self$stat$setup_params(data, self$stat_params)
16. │ └─ggplot2 (local) setup_params(...)
17. │ └─rlang::check_installed("MASS", "for calculating ellipses with `type = \"t\"`.")
18. │ └─base::stop(cnd)
19. └─rlang (local) `<fn>`(`<rlb_r___>`)
20. └─handlers[[1L]](cnd)
21. └─cli::cli_abort(...)
22. └─rlang::abort(...)
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 0.0.25
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘o2plsda.Rmd’ using knitr
Quitting from o2plsda.Rmd:91-96 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'o2plsda.Rmd' failed with diagnostics:
Problem while computing stat.
ℹ Error occurred in the 3rd layer.
Caused by error in `setup_params()`:
! The package "MASS" is required for calculating ellipses with `type =
"t"`.
--- failed re-building ‘o2plsda.Rmd’
SUMMARY: processing the following file failed:
‘o2plsda.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64