##############################################################################
##############################################################################
###
### 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