| Back to Build/check report for BioC 3.23: simplified long |
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This page was generated on 2026-02-06 11:32 -0500 (Fri, 06 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" | 4857 |
| 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 361/2347 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cicero 1.29.0 (landing page) Hannah Pliner
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| See other builds for cicero in R Universe. | ||||||||||||||
|
To the developers/maintainers of the cicero package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cicero.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: cicero |
| Version: 1.29.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data cicero |
| StartedAt: 2026-02-05 16:50:10 -0500 (Thu, 05 Feb 2026) |
| EndedAt: 2026-02-05 16:51:26 -0500 (Thu, 05 Feb 2026) |
| EllapsedTime: 76.1 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 cicero
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* checking for file ‘cicero/DESCRIPTION’ ... OK
* preparing ‘cicero’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘website.Rmd’ using rmarkdown
Quitting from website.Rmd:475-488 [unnamed-chunk-13]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/lifecycle_error_deprecated>
Error:
! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
---
Backtrace:
▆
1. ├─BiocGenerics::estimateDispersions(agg_cds)
2. └─monocle (local) estimateDispersions(agg_cds)
3. └─monocle (local) .local(object, ...)
4. └─monocle:::estimateDispersionsForCellDataSet(...)
5. └─dplyr::group_by_(...)
6. └─dplyr:::lazy_defunct("group_by")
7. └─lifecycle::deprecate_stop(...)
8. └─lifecycle:::deprecate_stop0(msg)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'website.Rmd' failed with diagnostics:
`group_by_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
--- failed re-building ‘website.Rmd’
SUMMARY: processing the following file failed:
‘website.Rmd’
Error: Vignette re-building failed.
Execution halted