Build/check report for BioC 3.23 - BUILD results for fgsea on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4994
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BUILD results for fgsea on nebbiolo1

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

Version: 1.38.0

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

StartedAt: 2026-05-12 17:45:33 -0400 (Tue, 12 May 2026)

EndedAt: 2026-05-12 17:50:06 -0400 (Tue, 12 May 2026)

EllapsedTime: 272.4 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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

--- re-building ‘geseca-tutorial.Rmd’ using rmarkdown

Quitting from geseca-tutorial.Rmd:319-327 [unnamed-chunk-23]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Caught an unexpected error of class FutureLaunchError when trying to launch future ('future_lapply-1') on backend of class SequentialFutureBackend. The reason was: future::evalFuture() failed on nebbiolo1 (pid 2937894) at 2026-05-12T17:50:04. Using package 'future' v1.70.0. Possible other reasons: protect(): protection stack overflow [future 'future_lapply-1' (5fe3c2dc8315479c4780132033b14ba3-7); on 5fe3c2dc8315479c4780132033b14ba3@nebbiolo1<2937894>]
---
Backtrace:
     ▆
  1. ├─Seurat::SCTransform(...)
  2. └─Seurat:::SCTransform.Seurat(...)
  3.   ├─Seurat::SCTransform(...)
  4.   └─Seurat:::SCTransform.StdAssay(...)
  5.     └─base::lapply(...)
  6.       └─Seurat (local) FUN(X[[i]], ...)
  7.         ├─Seurat::SCTransform(...)
  8.         └─Seurat:::SCTransform.Assay(...)
  9.           ├─Seurat::SCTransform(...)
 10.           └─Seurat:::SCTransform.default(...)
 11.             ├─base::do.call(what = "vst", args = vst.args)
 12.             └─sctransform::vst(...)
 13.               └─sctransform:::get_model_pars(...)
 14.                 └─future.apply::future_lapply(...)
 15.                   └─future.apply:::future_xapply(...)
 16.                     └─base::tryCatch(...)
 17.                       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 18.                         └─base (local) tryCatchOne(...)
 19.                           └─value[[3L]](cond)
 20.                             └─future.apply:::onError(e, futures = fs, debug = debug)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'geseca-tutorial.Rmd' failed with diagnostics:
Caught an unexpected error of class FutureLaunchError when trying to launch future ('future_lapply-1') on backend of class SequentialFutureBackend. The reason was: future::evalFuture() failed on nebbiolo1 (pid 2937894) at 2026-05-12T17:50:04. Using package 'future' v1.70.0. Possible other reasons: protect(): protection stack overflow [future 'future_lapply-1' (5fe3c2dc8315479c4780132033b14ba3-7); on 5fe3c2dc8315479c4780132033b14ba3@nebbiolo1<2937894>]
--- failed re-building ‘geseca-tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘geseca-tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted