Multiple platform build/check report for BioC 3.22 - BUILD results for slingshot on taishan

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 slingshot on taishan

To the developers/maintainers of the slingshot package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/slingshot.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: slingshot

Version: 2.17.0

Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data slingshot

StartedAt: 2025-08-12 02:53:41 -0000 (Tue, 12 Aug 2025)

EndedAt: 2025-08-12 02:54:45 -0000 (Tue, 12 Aug 2025)

EllapsedTime: 64.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data slingshot
###
##############################################################################
##############################################################################


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

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

Quitting from vignette.Rmd:275-277 [sling_sce]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `mst()`:
! At vendor/cigraph/src/misc/spanning_trees.c:283 : Weigths must not contain NaN values. Invalid value
---
Backtrace:
     ▆
  1. ├─slingshot::slingshot(sce, clusterLabels = "GMM", reducedDim = "PCA")
  2. └─slingshot::slingshot(sce, clusterLabels = "GMM", reducedDim = "PCA")
  3.   └─slingshot (local) .local(data, clusterLabels, ...)
  4.     ├─slingshot::slingshot(...)
  5.     └─slingshot::slingshot(...)
  6.       ├─slingshot::slingshot(...)
  7.       └─slingshot::slingshot(...)
  8.         └─slingshot (local) .local(data, clusterLabels, ...)
  9.           ├─slingshot::getLineages(...)
 10.           └─slingshot::getLineages(...)
 11.             ├─slingshot::getLineages(...)
 12.             └─slingshot::getLineages(...)
 13.               └─slingshot (local) .local(data, clusterLabels, ...)
 14.                 ├─TrajectoryUtils::createClusterMST(...)
 15.                 └─TrajectoryUtils::createClusterMST(...)
 16.                   └─TrajectoryUtils (local) .local(x, ...)
 17.                     └─igraph::minimum.spanning.tree(g)
 18.                       └─igraph::mst(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'vignette.Rmd' failed with diagnostics:
At vendor/cigraph/src/misc/spanning_trees.c:283 : Weigths must not contain NaN values. Invalid value
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted