Multiple platform build/check report for BioC 3.22 - BUILD results for scp on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4818
palomino8	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4553
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4595
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4537
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4535
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 scp on nebbiolo2

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

Version: 1.19.3

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 scp

StartedAt: 2025-08-13 19:24:40 -0400 (Wed, 13 Aug 2025)

EndedAt: 2025-08-13 19:28:27 -0400 (Wed, 13 Aug 2025)

EllapsedTime: 227.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 scp
###
##############################################################################
##############################################################################


* checking for file ‘scp/DESCRIPTION’ ... OK
* preparing ‘scp’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘QFeatures_nutshell.Rmd’ using rmarkdown

Quitting from QFeatures_nutshell.Rmd:353-360 [longForm]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.matchAddColData()`:
! argument "check.names" is missing, with no default
---
Backtrace:
    ▆
 1. ├─BiocGenerics::longForm(...)
 2. └─QFeatures::longForm(scp1[, , 1], colvars = c("SampleType", "Channel"))
 3.   └─QFeatures (local) .local(object, ...)
 4.     └─QFeatures:::longFormQFeatures(object, colvars, rowvars, i)
 5.       ├─MultiAssayExperiment::longForm(...)
 6.       └─MultiAssayExperiment::longForm(...)
 7.         └─MultiAssayExperiment (local) .local(object, ...)
 8.           └─MultiAssayExperiment:::.matchAddColData(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'QFeatures_nutshell.Rmd' failed with diagnostics:
argument "check.names" is missing, with no default
--- failed re-building ‘QFeatures_nutshell.Rmd’

--- re-building ‘advanced.Rmd’ using rmarkdown
--- finished re-building ‘advanced.Rmd’

--- re-building ‘read_scp.Rmd’ using rmarkdown
--- finished re-building ‘read_scp.Rmd’

--- re-building ‘reporting_missing_values.Rmd’ using rmarkdown
--- finished re-building ‘reporting_missing_values.Rmd’

--- re-building ‘scp.Rmd’ using rmarkdown

Quitting from scp.Rmd:985-1007 [monitor_plot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.matchAddColData()`:
! argument "check.names" is missing, with no default
---
Backtrace:
     ▆
  1. ├─ggplot2::ggplot(...)
  2. ├─dplyr::mutate(...)
  3. ├─base::data.frame(...)
  4. ├─BiocGenerics::longForm(...)
  5. └─QFeatures::longForm(...)
  6.   └─QFeatures (local) .local(object, ...)
  7.     └─QFeatures:::longFormQFeatures(object, colvars, rowvars, i)
  8.       ├─MultiAssayExperiment::longForm(...)
  9.       └─MultiAssayExperiment::longForm(...)
 10.         └─MultiAssayExperiment (local) .local(object, ...)
 11.           └─MultiAssayExperiment:::.matchAddColData(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'scp.Rmd' failed with diagnostics:
argument "check.names" is missing, with no default
--- failed re-building ‘scp.Rmd’

--- re-building ‘scp_data_modelling.Rmd’ using rmarkdown
Warning: ggrepel: 13 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘scp_data_modelling.Rmd’

SUMMARY: processing the following files failed:
  ‘QFeatures_nutshell.Rmd’ ‘scp.Rmd’

Error: Vignette re-building failed.
Execution halted