| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-21 11:32 -0500 (Sat, 21 Feb 2026).
| 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" | 4871 |
| 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 | ||||
| Package 739/2354 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| fgsea 1.37.4 (landing page) Alexey Sergushichev
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| See other builds for fgsea in R Universe. | ||||||||||||||
|
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. |
| Package: fgsea |
| Version: 1.37.4 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data fgsea |
| StartedAt: 2026-02-20 17:39:21 -0500 (Fri, 20 Feb 2026) |
| EndedAt: 2026-02-20 17:44:38 -0500 (Fri, 20 Feb 2026) |
| EllapsedTime: 317.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /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 2055377) at 2026-02-20T17:44:37. Using package 'future' v1.69.0. Possible other reasons: protect(): protection stack overflow [future 'future_lapply-1' (7a1e9cbf0ade34840e8836873328cb26-5); on 7a1e9cbf0ade34840e8836873328cb26@nebbiolo1<2055377>]
---
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 2055377) at 2026-02-20T17:44:37. Using package 'future' v1.69.0. Possible other reasons: protect(): protection stack overflow [future 'future_lapply-1' (7a1e9cbf0ade34840e8836873328cb26-5); on 7a1e9cbf0ade34840e8836873328cb26@nebbiolo1<2055377>]
--- failed re-building ‘geseca-tutorial.Rmd’
SUMMARY: processing the following file failed:
‘geseca-tutorial.Rmd’
Error: Vignette re-building failed.
Execution halted