Build/check report for BioC 3.24 - BUILD results for spatialHeatmap on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4890
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BUILD results for spatialHeatmap on nebbiolo2

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

Version: 2.19.1

Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 spatialHeatmap

StartedAt: 2026-05-08 20:22:51 -0400 (Fri, 08 May 2026)

EndedAt: 2026-05-08 20:26:21 -0400 (Fri, 08 May 2026)

EllapsedTime: 210.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 spatialHeatmap
###
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* checking for file ‘spatialHeatmap/DESCRIPTION’ ... OK
* preparing ‘spatialHeatmap’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to process help pages)
* saving partial Rd database
* creating vignettes ... ERROR
--- re-building ‘covisualize.Rmd’ using rmarkdown

Quitting from covisualize.Rmd:413-419 [unnamed-chunk-28]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to find an inherited method for function 'bindCOLS' for signature 'x = "matrix"'
---
Backtrace:
     ▆
  1. └─spatialHeatmap::cocluster(...)
  2.   └─BiocGenerics::cbind(blk.kp, sc.kp)
  3.     ├─BiocGenerics (local) standardGeneric("cbind")
  4.     │ ├─BiocGenerics::eval(mc, env)
  5.     │ └─base::eval(mc, env)
  6.     │   └─base::eval(mc, env)
  7.     └─SingleCellExperiment::cbind(...)
  8.       ├─methods::callNextMethod()
  9.       └─SummarizedExperiment (local) .nextMethod(... = ...)
 10.         └─SummarizedExperiment:::.cbind.SummarizedExperiment(args)
 11.           ├─BiocGenerics::do.call(cbind, lapply(args, slot, "assays"))
 12.           ├─base::do.call(cbind, lapply(args, slot, "assays"))
 13.           └─BiocGenerics (local) `<stndrdGn>`(`<SmplAssy[,4]>`, `<SmplAssy[,4454]>`)
 14.             ├─BiocGenerics (local) standardGeneric("cbind")
 15.             │ ├─BiocGenerics::eval(mc, env)
 16.             │ └─base::eval(mc, env)
 17.             │   └─base::eval(mc, env)
 18.             └─SummarizedExperiment::cbind(...)
 19.               └─SummarizedExperiment:::.bind_Assays_objects(objects, along.cols = TRUE)
 20.                 ├─BiocGenerics::lapply(...)
 21.                 └─base::lapply(...)
 22.                   └─SummarizedExperiment (local) FUN(X[[i]], ...)
 23.                     └─SummarizedExperiment:::.bind_assays(assays, along.cols = along.cols)
 24.                       ├─BiocGenerics::do.call(BINDING_FUN, assays)
 25.                       ├─base::do.call(BINDING_FUN, assays)
 26.                       └─BiocGenerics::cbind(`<dbl[,4]>`, `<DlydMtrx[,4454]>`)
 27.                         ├─BiocGenerics (local) standardGeneric("cbind")
 28.                         │ ├─BiocGenerics::eval(mc, env)
 29.                         │ └─base::eval(mc, env)
 30.                         │   └─base::eval(mc, env)
 31.                         └─base::cbind(...)
 32.                           └─S4Vectors::cbind(deparse.level, ...)
 33.                             └─S4Vectors::bindCOLS(objects[[1L]], objects = objects[-1L])
 34.                               └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'covisualize.Rmd' failed with diagnostics:
unable to find an inherited method for function 'bindCOLS' for signature 'x = "matrix"'
--- failed re-building ‘covisualize.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted