Multiple platform build/check report for BioC 3.21 - BUILD results for limpca on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4827
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4608
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4549
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4581
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

BUILD results for limpca on kjohnson1

To the developers/maintainers of the limpca package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/limpca.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: limpca

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data limpca

StartedAt: 2025-09-23 03:08:49 -0400 (Tue, 23 Sep 2025)

EndedAt: 2025-09-23 03:10:24 -0400 (Tue, 23 Sep 2025)

EllapsedTime: 95.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data limpca
###
##############################################################################
##############################################################################


* checking for file ‘limpca/DESCRIPTION’ ... OK
* preparing ‘limpca’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Trout.Rmd’ using rmarkdown
2025-09-23 03:09:32.268 R[86651:396381277] XType: Using static font registry.
Warning: ggrepel: 63 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 71 unlabeled data points (too many overlaps). Consider increasing max.overlaps

Quitting from Trout.Rmd:310-317 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `S7::prop(x, "meta")[[i]]`:
! subscript out of bounds
---
Backtrace:
    ▆
 1. └─limpca::pcaLoading1dPlot(...)
 2.   ├─fig[[1]]
 3.   └─ggplot2 (local) `[[.ggplot2::gg`(fig, 1)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Trout.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘Trout.Rmd’

--- re-building ‘UCH.Rmd’ using rmarkdown

Quitting from UCH.Rmd:294-302 [Loadings]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `S7::prop(x, "meta")[[i]]`:
! subscript out of bounds
---
Backtrace:
    ▆
 1. └─limpca::pcaLoading1dPlot(...)
 2.   ├─fig[[1]]
 3.   └─ggplot2 (local) `[[.ggplot2::gg`(fig, 1)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'UCH.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘UCH.Rmd’

--- re-building ‘limpca.Rmd’ using rmarkdown
--- finished re-building ‘limpca.Rmd’

SUMMARY: processing the following files failed:
  ‘Trout.Rmd’ ‘UCH.Rmd’

Error: Vignette re-building failed.
Execution halted