Multiple platform build/check report for BioC 3.21 - BUILD results for scDiagnostics on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4609
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4393
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	3839
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	3835
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4408
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 lconway

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: 1.1.0

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

StartedAt: 2025-01-23 17:21:29 -0500 (Thu, 23 Jan 2025)

EndedAt: 2025-01-23 17:23:32 -0500 (Thu, 23 Jan 2025)

EllapsedTime: 122.1 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 scDiagnostics
###
##############################################################################
##############################################################################


* checking for file ‘scDiagnostics/DESCRIPTION’ ... OK
* preparing ‘scDiagnostics’:
* checking DESCRIPTION meta-information ... OK
* installing the package 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
2025-01-23 17:22:13.044 R[97554:981485993] XType: com.apple.fonts is not accessible.
2025-01-23 17:22:13.045 R[97554:981485993] XType: XTFontStaticRegistry is enabled.
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 lines 118-140 [unnamed-chunk-2] (DatasetMarkerGeneAlignment.Rmd)
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 lines 189-211 [unnamed-chunk-5] (scDiagnostics.Rmd)
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