Multiple platform build/check report for BioC 3.23 - BUILD results for VplotR on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences"	4808
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4593
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 VplotR on nebbiolo1

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

Version: 1.21.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data VplotR

StartedAt: 2025-12-30 20:40:07 -0500 (Tue, 30 Dec 2025)

EndedAt: 2025-12-30 20:41:39 -0500 (Tue, 30 Dec 2025)

EllapsedTime: 92.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data VplotR
###
##############################################################################
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* checking for file ‘VplotR/DESCRIPTION’ ... OK
* preparing ‘VplotR’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘VplotR.Rmd’ using rmarkdown

Quitting from VplotR.Rmd:229-249 [unnamed-chunk-12]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `do.call()`:
! replacement has length zero
---
Backtrace:
     ▆
  1. ├─VplotR::plotVmat(...)
  2. └─VplotR:::plotVmat.list(...)
  3.   └─parallel::mclapply(...)
  4.     └─base::lapply(X = X, FUN = FUN, ...)
  5.       └─VplotR (local) FUN(X[[i]], ...)
  6.         ├─VplotR::plotVmat(...)
  7.         └─VplotR:::plotVmat.GRanges(...)
  8.           └─VplotR::computeVmat(...)
  9.             ├─methods (local) `[<-`(`*tmp*`, filt, value = `<GRanges>`)
 10.             └─S4Vectors (local) `[<-`(`*tmp*`, filt, value = `<GRanges>`)
 11.               ├─methods::callNextMethod(x, i, value = value)
 12.               │ └─base::eval(call, callEnv)
 13.               │   └─base::eval(call, callEnv)
 14.               └─S4Vectors (local) .nextMethod(x, i, value = value)
 15.                 ├─S4Vectors::mergeROWS(x, i, value)
 16.                 └─S4Vectors::mergeROWS(x, i, value)
 17.                   ├─S4Vectors::replaceROWS(x, nsbs, value)
 18.                   └─GenomicRanges (local) replaceROWS(x, nsbs, value)
 19.                     ├─S4Vectors::replaceROWS(...)
 20.                     └─S4Vectors::replaceROWS(...)
 21.                       └─S4Vectors:::.subassign_columns(x, nsbs, value)
 22.                         ├─BiocGenerics::lapply(...)
 23.                         └─base::lapply(...)
 24.                           └─S4Vectors (local) FUN(X[[i]], ...)
 25.                             ├─S4Vectors (local) FUN(x[[j]], nsbs, value[[((j - 1L)%%value_ncol) + 1L]])
 26.                             └─S4Vectors (local) FUN(x[[j]], nsbs, value[[((j - 1L)%%value_ncol) + 1L]])
 27.                               ├─S4Vectors::mergeROWS(x, i, value)
 28.                               └─S4Vectors::mergeROWS(x, i, value)
 29.                                 ├─BiocGenerics::do.call(`[<-`, args)
 30.                                 └─base::do.call(`[<-`, args)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'VplotR.Rmd' failed with diagnostics:
replacement has length zero
--- failed re-building ‘VplotR.Rmd’

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

Error: Vignette re-building failed.
Execution halted