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This page was generated on 2025-11-13 11:32 -0500 (Thu, 13 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4013 |
| 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 2081/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SPONGE 1.33.0 (landing page) Markus List
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | ||||||||
|
To the developers/maintainers of the SPONGE package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SPONGE.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: SPONGE |
| Version: 1.33.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SPONGE |
| StartedAt: 2025-11-12 17:18:26 -0500 (Wed, 12 Nov 2025) |
| EndedAt: 2025-11-12 17:19:44 -0500 (Wed, 12 Nov 2025) |
| EllapsedTime: 78.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SPONGE
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* checking for file ‘SPONGE/DESCRIPTION’ ... OK
* preparing ‘SPONGE’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘SPONGE.Rmd’ using rmarkdown
2025-11-12 17:19:27.067 R[24733:3515736] XType: Using static font registry.
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "SPONGE vignette", and the latter is "Sparse Partial correlation ON Gene Expression with SPONGE". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘SPONGE.Rmd’
--- re-building ‘spongEffects.Rmd’ using rmarkdown
Quitting from spongEffects.Rmd:127-131 [unnamed-chunk-13]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `e$fun()`:
! worker initialization failed: there is no package called ‘GSVA’
---
Backtrace:
▆
1. └─SPONGE::enrichment_modules(...)
2. └─... %dopar% ...
3. └─e$fun(obj, substitute(ex), parent.frame(), e$data)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'spongEffects.Rmd' failed with diagnostics:
worker initialization failed: there is no package called ‘GSVA’
--- failed re-building ‘spongEffects.Rmd’
SUMMARY: processing the following file failed:
‘spongEffects.Rmd’
Error: Vignette re-building failed.
Execution halted