Multiple platform build/check report for BioC 3.21 - BUILD results for FlowSOM on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4831
palomino7	Windows Server 2022 Datacenter	x64	4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"	4573
lconway	macOS 12.7.1 Monterey	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4599
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4553
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4570
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 FlowSOM on kjohnson3

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

Version: 2.16.0

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

StartedAt: 2025-04-17 16:22:21 -0400 (Thu, 17 Apr 2025)

EndedAt: 2025-04-17 16:22:49 -0400 (Thu, 17 Apr 2025)

EllapsedTime: 28.3 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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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 FlowSOM
###
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* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* preparing ‘FlowSOM’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘FlowSOM.Rnw’ using Sweave
Loading required package: igraph

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

Thanks for using FlowSOM. From version 2.1.4 on, the scale 
parameter in the FlowSOM function defaults to FALSE
Plot FlowSOM trees
Calculate t-SNE
Plot cluster per metacluster distribution
Plot heatmap
Make tables
Printing

Attaching package: ‘flowCore’

The following object is masked from ‘package:igraph’:

    normalize

Reading file /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp2UTYYc/Rinst10d8b694d9764/FlowSOM/extdata/68983.fcs

Scaling the data

Scaling the data

Building SOM

Mapping data to SOM

Building MST

The packages "CytoML" and "flowWorkspace" are necessary for the function GetFlowJoLabels, but are not available.

Error: processing vignette 'FlowSOM.Rnw' failed with diagnostics:
 chunk 17 
Error in PlotPies(fSOM, cellTypes = gatingResult$manual) : 
  There are 19225 cells, while you provided 0 labels. These numbers should match.

--- failed re-building ‘FlowSOM.Rnw’

SUMMARY: processing the following file failed:
  ‘FlowSOM.Rnw’

Error: Vignette re-building failed.
Execution halted