Multiple platform build/check report for BioC 3.21 - BUILD results for pathlinkR on kunpeng2

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"	4833
merida1	macOS 12.7.6 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4614
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4555
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4586
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 pathlinkR on kunpeng2

To the developers/maintainers of the pathlinkR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pathlinkR.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: pathlinkR

Version: 1.4.0

Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data pathlinkR

StartedAt: 2025-10-14 03:24:43 -0000 (Tue, 14 Oct 2025)

EndedAt: 2025-10-14 03:27:44 -0000 (Tue, 14 Oct 2025)

EllapsedTime: 180.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data pathlinkR
###
##############################################################################
##############################################################################


* checking for file ‘pathlinkR/DESCRIPTION’ ... OK
* preparing ‘pathlinkR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘pathlinkR.Rmd’ using rmarkdown
Warning: ggrepel: 37 unlabeled data points (too many overlaps). Consider increasing max.overlaps

Quitting from pathlinkR.Rmd:297-302 [plot_pathways_I]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `space$x`:
! $ operator is invalid for atomic vectors
---
Backtrace:
     ▆
  1. └─pathlinkR::pathwayPlots(...)
  2.   └─ggpubr::ggarrange(...)
  3.     └─ggpubr::get_legend(plots)
  4.       └─ggpubr:::.get_legend(p[[i]], position = position)
  5.         ├─ggplot2::ggplot_gtable(ggplot_build(p))
  6.         └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(ggplot_build(p))
  7.           └─layout$render(geom_grobs, data, theme, plot@labels)
  8.             └─ggplot2 (local) render(..., self = self)
  9.               └─self$facet$draw_panels(...)
 10.                 └─ggforce (local) draw_panels(..., self = self)
 11.                   └─ggproto_parent(FacetWrap, self)$draw_panels(...)
 12.                     └─ggplot2 (local) draw_panels(..., self = self)
 13.                       └─ggproto_parent(Facet, self)$draw_panels(...)
 14.                         └─ggplot2 (local) draw_panels(..., self = self)
 15.                           └─self$init_gtable(...)
 16.                             └─ggplot2 (local) init_gtable(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'pathlinkR.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘pathlinkR.Rmd’

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

Error: Vignette re-building failed.
Execution halted