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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4869
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4576
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 crisprDesign on kjohnson3

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

Version: 1.13.6

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

StartedAt: 2025-12-03 16:03:28 -0500 (Wed, 03 Dec 2025)

EndedAt: 2025-12-03 16:04:08 -0500 (Wed, 03 Dec 2025)

EllapsedTime: 40.4 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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


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

Quitting from baseEditing.Rmd:159-167 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `ij[[2]]`:
! subscript out of bounds
---
Backtrace:
    ▆
 1. └─crisprDesign::addEditedAlleles(...)
 2.   └─base::lapply(alleles, .addFunctionalConsequences, txTable)
 3.     └─crisprDesign (local) FUN(X[[i]], ...)
 4.       └─crisprDesign:::.closestCdsCoordinate(nonoverlapPositions, txTable$pos)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'baseEditing.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘baseEditing.Rmd’

--- re-building ‘intro.Rmd’ using rmarkdown
# reads processed: 20
# reads with at least one alignment: 20 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 20 alignments

Quitting from intro.Rmd:747-753 [unnamed-chunk-36]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `ij[[2]]`:
! subscript out of bounds
---
Backtrace:
    ▆
 1. └─crisprDesign::addEditedAlleles(...)
 2.   └─base::lapply(alleles, .addFunctionalConsequences, txTable)
 3.     └─crisprDesign (local) FUN(X[[i]], ...)
 4.       └─crisprDesign:::.closestCdsCoordinate(nonoverlapPositions, txTable$pos)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'intro.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following files failed:
  ‘baseEditing.Rmd’ ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted