Multiple platform build/check report for BioC 3.21 - BUILD results for miloR on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4827
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4608
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4549
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4581
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 miloR on kjohnson1

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

Version: 2.4.1

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

StartedAt: 2025-09-23 04:20:01 -0400 (Tue, 23 Sep 2025)

EndedAt: 2025-09-23 04:41:18 -0400 (Tue, 23 Sep 2025)

EllapsedTime: 1277.1 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 miloR
###
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* checking for file ‘miloR/DESCRIPTION’ ... OK
* preparing ‘miloR’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘milo_contrasts.Rmd’ using rmarkdown
2025-09-23 04:24:02.029 R[9243:396621269] XType: Using static font registry.
--- finished re-building ‘milo_contrasts.Rmd’

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

--- re-building ‘milo_gastrulation.Rmd’ using rmarkdown
Warning: ggrepel: 4 unlabeled data points (too many overlaps). Consider increasing max.overlaps

Quitting from milo_gastrulation.Rmd:420-426 [unnamed-chunk-36]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.local()`:
! non-conformable arguments
---
Backtrace:
    ▆
 1. └─miloR::plotNhoodExpressionGroups(...)
 2.   └─miloR::calcNhoodExpression(x, assay = assay, subset.row = features)
 3.     └─miloR:::.calc_expression(...)
 4.       ├─Matrix::tcrossprod(...)
 5.       └─Matrix::tcrossprod(...)
 6.         └─Matrix (local) .local(x, y, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'milo_gastrulation.Rmd' failed with diagnostics:
non-conformable arguments
--- failed re-building ‘milo_gastrulation.Rmd’

--- re-building ‘milo_glmm.Rmd’ using rmarkdown
Warning: call dbDisconnect() when finished working with a connection
--- finished re-building ‘milo_glmm.Rmd’

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

Error: Vignette re-building failed.
Execution halted