| Back to Multiple platform build/check report for BioC 3.23: simplified long |
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This page was generated on 2026-01-21 11:34 -0500 (Wed, 21 Jan 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" | 4805 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4539 |
| 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 764/2343 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FlowSOM 2.19.2 (landing page) Sofie Van Gassen
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
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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. |
| Package: FlowSOM |
| Version: 2.19.2 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data FlowSOM |
| StartedAt: 2026-01-20 17:40:59 -0500 (Tue, 20 Jan 2026) |
| EndedAt: 2026-01-20 17:42:13 -0500 (Tue, 20 Jan 2026) |
| EllapsedTime: 74.1 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 FlowSOM
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* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* preparing ‘FlowSOM’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed 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 /tmp/Rtmp4nH4Jf/Rinst1bd21877ea66bc/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