| Back to Build/check report for BioC 3.23: simplified long |
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This page was generated on 2026-02-05 11:32 -0500 (Thu, 05 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" | 4852 |
| 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 1649/2347 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PRONE 1.5.0 (landing page) Lis Arend
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| See other builds for PRONE in R Universe. | ||||||||||||||
|
To the developers/maintainers of the PRONE package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PRONE.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: PRONE |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data PRONE |
| StartedAt: 2026-02-04 19:26:12 -0500 (Wed, 04 Feb 2026) |
| EndedAt: 2026-02-04 19:27:56 -0500 (Wed, 04 Feb 2026) |
| EllapsedTime: 104.1 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 PRONE
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* checking for file ‘PRONE/DESCRIPTION’ ... OK
* preparing ‘PRONE’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘Differential_Expression.Rmd’ using rmarkdown
--- finished re-building ‘Differential_Expression.Rmd’
--- re-building ‘Imputation.Rmd’ using rmarkdown
--- finished re-building ‘Imputation.Rmd’
--- re-building ‘Normalization.Rmd’ using rmarkdown
--- finished re-building ‘Normalization.Rmd’
--- re-building ‘PRONE.Rmd’ using rmarkdown
--- finished re-building ‘PRONE.Rmd’
--- re-building ‘Preprocessing.Rmd’ using rmarkdown
--- finished re-building ‘Preprocessing.Rmd’
--- re-building ‘Spike_In_Data.Rmd’ using rmarkdown
Quitting from Spike_In_Data.Rmd:96-98 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/lifecycle_error_deprecated>
Error:
! `summarise_each()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `across()` instead.
---
Backtrace:
▆
1. ├─PRONE::plot_identified_spiked_proteins(se)
2. │ └─dt %>% dplyr::group_by(Spiked) %>% ...
3. └─dplyr::summarise_each(., dplyr::funs(sum))
4. └─dplyr:::each_defunct("summarise_each()")
5. └─lifecycle::deprecate_stop(when = "0.7.0", what = fun, with = "across()")
6. └─lifecycle:::deprecate_stop0(msg)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Spike_In_Data.Rmd' failed with diagnostics:
`summarise_each()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `across()` instead.
--- failed re-building ‘Spike_In_Data.Rmd’
SUMMARY: processing the following file failed:
‘Spike_In_Data.Rmd’
Error: Vignette re-building failed.
Execution halted