Multiple platform build/check report for BioC 3.20 - BUILD results for MAGeCKFlute on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4756
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4514
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4441
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4406
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 MAGeCKFlute on palomino8

To the developers/maintainers of the MAGeCKFlute package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MAGeCKFlute.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: MAGeCKFlute

Version: 2.10.0

Command: chmod a+r MAGeCKFlute -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data MAGeCKFlute

StartedAt: 2025-03-17 19:50:35 -0400 (Mon, 17 Mar 2025)

EndedAt: 2025-03-17 19:56:33 -0400 (Mon, 17 Mar 2025)

EllapsedTime: 358.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r MAGeCKFlute -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data MAGeCKFlute
###
##############################################################################
##############################################################################


* checking for file 'MAGeCKFlute/DESCRIPTION' ... OK
* preparing 'MAGeCKFlute':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'MAGeCKFlute.Rmd' using rmarkdown
Warning: ggrepel: 5 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning: ggrepel: 3 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 5 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 10 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 5 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building 'MAGeCKFlute.Rmd'

--- re-building 'MAGeCKFlute_enrichment.Rmd' using rmarkdown

Quitting from MAGeCKFlute_enrichment.Rmd:103-110 [enrichplot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `get()`:
! invalid first argument
---
Backtrace:
     ▆
  1. ├─ggtangle::cnetplot(hgtRes1, 5)
  2. └─enrichplot:::cnetplot.enrichResult(hgtRes1, 5)
  3.   ├─ggtangle::cnetplot(...)
  4.   └─ggtangle:::cnetplot.list(...)
  5.     ├─ggplot2::ggplot(g, layout = layout)
  6.     └─ggtangle:::ggplot.igraph(g, layout = layout)
  7.       └─ggtangle:::get_igraph_layout(layout)
  8.         └─yulab.utils::get_fun_from_pkg("igraph", layout)
  9.           └─utils::getFromNamespace(fun, pkg)
 10.             └─base::get(x, envir = ns, inherits = FALSE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MAGeCKFlute_enrichment.Rmd' failed with diagnostics:
invalid first argument
--- failed re-building 'MAGeCKFlute_enrichment.Rmd'

SUMMARY: processing the following file failed:
  'MAGeCKFlute_enrichment.Rmd'

Error: Vignette re-building failed.
Execution halted