Build/check report for BioC 3.23 - BUILD results for concordexR on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4013
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 concordexR on kjohnson3

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

Version: 1.11.0

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

StartedAt: 2025-11-12 16:02:20 -0500 (Wed, 12 Nov 2025)

EndedAt: 2025-11-12 16:02:37 -0500 (Wed, 12 Nov 2025)

EllapsedTime: 16.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data concordexR
###
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* checking for file ‘concordexR/DESCRIPTION’ ... OK
* preparing ‘concordexR’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘concordex-nonspatial.Rmd’ using rmarkdown

Quitting from concordex-nonspatial.Rmd:44-53 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'TENxPBMCData'
---
Backtrace:
    ▆
 1. └─base::library(TENxPBMCData)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'concordex-nonspatial.Rmd' failed with diagnostics:
there is no package called 'TENxPBMCData'
--- failed re-building ‘concordex-nonspatial.Rmd’

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

Quitting from overview.Rmd:45-50 [example]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! failed to load resource
  name: EH7561
  title: Small demo subset of mouse skeletal muscle Visium data
  reason: require("SpatialFeatureExperiment") failed: use BiocManager::install() to install package?
---
Backtrace:
     ▆
  1. └─SFEData::McKellarMuscleData("small")
  2.   ├─ds[[id, force = force, verbose = verbose]]
  3.   └─ds[[id, force = force, verbose = verbose]]
  4.     └─ExperimentHub (local) .local(x, i, j = j, ...)
  5.       ├─methods::callNextMethod(...)
  6.       │ └─base::eval(call, callEnv)
  7.       │   └─base::eval(call, callEnv)
  8.       └─AnnotationHub (local) .nextMethod(...)
  9.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 10.           └─AnnotationHub:::.Hub_get1(...)
 11.             └─base::tryCatch(...)
 12.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 13.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 14.                   └─value[[3L]](cond)
 15.                     └─base::tryCatch(...)
 16.                       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 17.                         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 18.                           └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'overview.Rmd' failed with diagnostics:
failed to load resource
  name: EH7561
  title: Small demo subset of mouse skeletal muscle Visium data
  reason: require("SpatialFeatureExperiment") failed: use BiocManager::install() to install package?
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following files failed:
  ‘concordex-nonspatial.Rmd’ ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted