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

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

Version: 1.5.0

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

StartedAt: 2025-11-12 17:09:02 -0500 (Wed, 12 Nov 2025)

EndedAt: 2025-11-12 17:10:35 -0500 (Wed, 12 Nov 2025)

EllapsedTime: 93.1 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 scDiagnostics
###
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* checking for file ‘scDiagnostics/DESCRIPTION’ ... OK
* preparing ‘scDiagnostics’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘AnnotationAnomalies.Rmd’ using rmarkdown
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
2025-11-12 17:09:22.906 R[25545:3305148] XType: Using static font registry.
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
--- finished re-building ‘AnnotationAnomalies.Rmd’

--- re-building ‘DatasetMarkerGeneAlignment.Rmd’ using rmarkdown
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH

Quitting from DatasetMarkerGeneAlignment.Rmd:115-138 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'scran'
---
Backtrace:
    ▆
 1. └─base::library(scran)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

--- re-building ‘VisualizationTools.Rmd’ using rmarkdown
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
--- finished re-building ‘VisualizationTools.Rmd’

--- re-building ‘scDiagnostics.Rmd’ using rmarkdown
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH
Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { :
  cannot find pngquant; please install and put it in PATH

Quitting from scDiagnostics.Rmd:188-211 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'scran'
---
Backtrace:
    ▆
 1. └─base::library(scran)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

SUMMARY: processing the following files failed:
  ‘DatasetMarkerGeneAlignment.Rmd’ ‘scDiagnostics.Rmd’

Error: Vignette re-building failed.
Execution halted