Multiple platform build/check report for BioC 3.23 - BUILD results for tradeSeq 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"	4829
lconway	macOS 12.7.6 Monterey	x86_64	R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"	4602
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4566
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 tradeSeq on kjohnson3

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

Version: 1.25.0

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

StartedAt: 2025-11-20 17:59:48 -0500 (Thu, 20 Nov 2025)

EndedAt: 2025-11-20 18:02:19 -0500 (Thu, 20 Nov 2025)

EllapsedTime: 150.8 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 tradeSeq
###
##############################################################################
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* checking for file ‘tradeSeq/DESCRIPTION’ ... OK
* preparing ‘tradeSeq’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘Monocle.Rmd’ using rmarkdown
--- finished re-building ‘Monocle.Rmd’

--- re-building ‘fitGAM.Rmd’ using rmarkdown
2025-11-20 18:00:08.976 R[20555:100876389] XType: Using static font registry.

Quitting from fitGAM.Rmd:152-159 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `reducer$value.cache[[as.character(idx)]] <- values`:
! wrong args for environment subassignment
---
Backtrace:
     ▆
  1. ├─tradeSeq::fitGAM(...)
  2. └─tradeSeq::fitGAM(...)
  3.   └─tradeSeq (local) .local(counts, ...)
  4.     └─tradeSeq:::.fitGAM(...)
  5.       ├─BiocParallel::bplapply(...)
  6.       └─BiocParallel::bplapply(...)
  7.         └─BiocParallel:::.bpinit(...)
  8.           ├─BiocParallel::bploop(...)
  9.           └─BiocParallel:::bploop.lapply(...)
 10.             └─BiocParallel:::.bploop_impl(...)
 11.               └─BiocParallel:::.collect_result(manager, reducer, progress, BPPARAM)
 12.                 ├─BiocParallel:::.reducer_add(reducer, njob, value)
 13.                 └─BiocParallel:::.reducer_add(reducer, njob, value)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'fitGAM.Rmd' failed with diagnostics:
wrong args for environment subassignment
--- failed re-building ‘fitGAM.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted