Alexey Sergushichev
| Snapshot Date: 2026-05-18 13:45 -0400 (Mon, 18 May 2026) |
| git_url: https://git.bioconductor.org/packages/fgsea |
| git_branch: devel |
| git_last_commit: 814dad4 |
| git_last_commit_date: 2026-04-28 08:43:45 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-19 12:54 -0400 (Tue, 19 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4898 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There" | 4617 |
| 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 743/2377 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| fgsea 1.39.0 (landing page) Alexey Sergushichev
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | | |||||||||
| 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: 1.39.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 fgsea |
| StartedAt: 2026-05-18 17:44:28 -0400 (Mon, 18 May 2026) |
| EndedAt: 2026-05-18 17:49:06 -0400 (Mon, 18 May 2026) |
| EllapsedTime: 278.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 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 nebbiolo2 (pid 1661760) at 2026-05-18T17:49:05. Using package 'future' v1.70.0. Possible other reasons: protect(): protection stack overflow [future 'future_lapply-1' (bee9f696b1012b20439980977e3b9d32-7); on bee9f696b1012b20439980977e3b9d32@nebbiolo2<1661760>]
---
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 nebbiolo2 (pid 1661760) at 2026-05-18T17:49:05. Using package 'future' v1.70.0. Possible other reasons: protect(): protection stack overflow [future 'future_lapply-1' (bee9f696b1012b20439980977e3b9d32-7); on bee9f696b1012b20439980977e3b9d32@nebbiolo2<1661760>]
--- failed re-building ‘geseca-tutorial.Rmd’
SUMMARY: processing the following file failed:
‘geseca-tutorial.Rmd’
Error: Vignette re-building failed.
Execution halted