Multiple platform build/check report for BioC 3.23 - BUILD results for GENESIS 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"	4805
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4539
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 GENESIS on kjohnson3

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

Version: 2.41.0

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

StartedAt: 2026-01-20 16:24:44 -0500 (Tue, 20 Jan 2026)

EndedAt: 2026-01-20 16:25:09 -0500 (Tue, 20 Jan 2026)

EllapsedTime: 24.3 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 GENESIS
###
##############################################################################
##############################################################################


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

--- re-building ‘assoc_test_seq.Rmd’ using rmarkdown
2026-01-20 16:25:04.019 R[99337:784344559] XType: Using static font registry.

Quitting from assoc_test_seq.Rmd:181-189 [assoc_single]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
     ▆
  1. ├─GENESIS::assocTestSingle(...)
  2. └─GENESIS::assocTestSingle(...)
  3.   └─GENESIS (local) .local(gdsobj, ...)
  4.     ├─BiocParallel::bpiterate(...)
  5.     └─BiocParallel::bpiterate(...)
  6.       └─BiocParallel (local) .local(ITER, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS)
  7.         └─BiocParallel:::.bpinit(...)
  8.           ├─BiocParallel::bploop(...)
  9.           └─BiocParallel:::bploop.iterate(...)
 10.             └─BiocParallel:::.bploop_impl(...)
 11.               └─BiocParallel (local) ITER()
 12.                 └─GENESIS (local) ITER()
 13.                   ├─SeqVarTools::variantInfo(gdsobj, alleles = FALSE, expanded = TRUE)
 14.                   └─SeqVarTools::variantInfo(gdsobj, alleles = FALSE, expanded = TRUE)
 15.                     └─SeqVarTools (local) .local(gdsobj, ...)
 16.                       ├─x[, `:=`("allele.index", seq_len(.N)), by = "variant.id"]
 17.                       └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

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

Error: Vignette re-building failed.
Execution halted