Multiple platform build/check report for BioC 3.22 - BUILD results for msqrob2 on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4749
palomino8	Windows Server 2022 Datacenter	x64	4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"	4511
lconway	macOS 12.7.1 Monterey	x86_64	4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"	4548
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"	4489
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4455
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*

BUILD results for msqrob2 on lconway

To the developers/maintainers of the msqrob2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/msqrob2.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.

raw results

Summary

Package: msqrob2

Version: 1.17.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data msqrob2

StartedAt: 2025-05-20 17:34:48 -0400 (Tue, 20 May 2025)

EndedAt: 2025-05-20 17:36:25 -0400 (Tue, 20 May 2025)

EllapsedTime: 97.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data msqrob2
###
##############################################################################
##############################################################################


* checking for file ‘msqrob2/DESCRIPTION’ ... OK
* preparing ‘msqrob2’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘cptac.Rmd’ using rmarkdown
2025-05-20 17:36:05.716 R[11755:51673637] XType: com.apple.fonts is not accessible.
2025-05-20 17:36:05.716 R[11755:51673637] XType: XTFontStaticRegistry is enabled.

Quitting from cptac.Rmd:306-344 [unnamed-chunk-21]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `lifeCycle()`:
! 'longFormat' is defunct.
  Use 'longForm' instead.
  See help('longFormat-defunct').
---
Backtrace:
    ▆
 1. ├─base::data.frame(longFormat(pePlot))
 2. └─QFeatures::longFormat(pePlot)
 3.   ├─MultiAssayExperiment::longFormat(object, colvars, index)
 4.   └─MultiAssayExperiment::longFormat(object, colvars, index)
 5.     ├─MultiAssayExperiment::longFormat(experiments(object), i = i)
 6.     └─MultiAssayExperiment::longFormat(experiments(object), i = i)
 7.       └─BiocBaseUtils::lifeCycle(...)
 8.         ├─base::do.call(cycle_fun, arglist)
 9.         └─base (local) `<fn>`(new = "longForm", msg = `<chr>`, package = "MultiAssayExperiment")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'cptac.Rmd' failed with diagnostics:
'longFormat' is defunct.
  Use 'longForm' instead.
  See help('longFormat-defunct').
--- failed re-building ‘cptac.Rmd’

SUMMARY: processing the following file failed:
  ‘cptac.Rmd’

Error: Vignette re-building failed.
Execution halted