Multiple platform build/check report for BioC 3.23 - BUILD results for maftools on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4808
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4542
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 maftools on kjohnson3

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

Version: 2.27.0

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

StartedAt: 2026-01-21 16:49:23 -0500 (Wed, 21 Jan 2026)

EndedAt: 2026-01-21 16:49:34 -0500 (Wed, 21 Jan 2026)

EllapsedTime: 11.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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


* checking for file ‘maftools/DESCRIPTION’ ... OK
* preparing ‘maftools’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘cancer_hotspots.Rmd’ using rmarkdown
--- finished re-building ‘cancer_hotspots.Rmd’

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

--- re-building ‘maftools.Rmd’ using rmarkdown
2026-01-21 16:49:33.044 R[7812:797966299] XType: Using static font registry.

Quitting from maftools.Rmd:131-133 [summaryPlot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
    ▆
 1. └─maftools::plotmafSummary(...)
 2.   └─maftools:::dashboard(...)
 3.     └─maftools::titv(maf = maf, useSyn = TRUE, plot = FALSE)
 4.       ├─...[]
 5.       └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'maftools.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘maftools.Rmd’

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

Quitting from oncoplots.Rmd:46-49 [insTiTv]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
    ▆
 1. └─maftools::oncoplot(maf = laml, draw_titv = TRUE)
 2.   └─maftools::titv(maf = maf, useSyn = TRUE, plot = FALSE)
 3.     ├─...[]
 4.     └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'oncoplots.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘oncoplots.Rmd’

SUMMARY: processing the following files failed:
  ‘maftools.Rmd’ ‘oncoplots.Rmd’

Error: Vignette re-building failed.
Execution halted