Multiple platform build/check report for BioC 3.23 - BUILD results for scDiagnostics on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 alpha (2026-04-05 r89794)	4917
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-03-26 r89717) -- "Unsuffered Consequences"	4629
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: 1.5.1

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

StartedAt: 2026-04-09 17:05:36 -0400 (Thu, 09 Apr 2026)

EndedAt: 2026-04-09 17:07:10 -0400 (Thu, 09 Apr 2026)

EllapsedTime: 94.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### 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 (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
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:
! package or namespace load failed for 'scran' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so, 0x0006): Symbol not found: _R_getRegisteredNamespace
  Referenced from: <D5FEE207-EB8F-3FC2-BC24-84E97E708ECA> /Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so
  Expected in:     <9885FFC9-0B1B-386C-8515-0CC182A63B5A> /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib
---
Backtrace:
    ▆
 1. └─base::library(scran)
 2.   └─base::tryCatch(...)
 3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5.         └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'DatasetMarkerGeneAlignment.Rmd' failed with diagnostics:
package or namespace load failed for 'scran' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so, 0x0006): Symbol not found: _R_getRegisteredNamespace
  Referenced from: <D5FEE207-EB8F-3FC2-BC24-84E97E708ECA> /Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so
  Expected in:     <9885FFC9-0B1B-386C-8515-0CC182A63B5A> /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib
--- 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

Quitting from VisualizationTools.Rmd:221-238 [unnamed-chunk-9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `dyn.load()`:
! unable to load shared object '/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so, 0x0006): Symbol not found: _R_getRegisteredNamespace
  Referenced from: <D5FEE207-EB8F-3FC2-BC24-84E97E708ECA> /Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so
  Expected in:     <9885FFC9-0B1B-386C-8515-0CC182A63B5A> /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib
---
Backtrace:
     ▆
  1. ├─scDiagnostics::calculateSIRSpace(...)
  2. │ └─scDiagnostics::projectSIR(...)
  3. │   └─scDiagnostics:::conditionalMeans(...)
  4. │     └─base::suppressWarnings(bluster::clusterRows(projections, BLUSPARAM = bluster::TwoStepParam(second = bluster::NNGraphParam(k = n_neighbor))))
  5. │       └─base::withCallingHandlers(...)
  6. └─base::loadNamespace(x)
  7.   ├─base::namespaceImportFrom(...)
  8.   │ └─base::asNamespace(ns)
  9.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
 10.     └─base::library.dynam(lib, package, package.lib)
 11.       └─base::dyn.load(file, DLLpath = DLLpath, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'VisualizationTools.Rmd' failed with diagnostics:
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so, 0x0006): Symbol not found: _R_getRegisteredNamespace
  Referenced from: <D5FEE207-EB8F-3FC2-BC24-84E97E708ECA> /Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so
  Expected in:     <9885FFC9-0B1B-386C-8515-0CC182A63B5A> /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib
--- failed 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:
! package or namespace load failed for 'scran' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so, 0x0006): Symbol not found: _R_getRegisteredNamespace
  Referenced from: <D5FEE207-EB8F-3FC2-BC24-84E97E708ECA> /Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so
  Expected in:     <9885FFC9-0B1B-386C-8515-0CC182A63B5A> /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib
---
Backtrace:
    ▆
 1. └─base::library(scran)
 2.   └─base::tryCatch(...)
 3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5.         └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'scDiagnostics.Rmd' failed with diagnostics:
package or namespace load failed for 'scran' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so, 0x0006): Symbol not found: _R_getRegisteredNamespace
  Referenced from: <D5FEE207-EB8F-3FC2-BC24-84E97E708ECA> /Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so
  Expected in:     <9885FFC9-0B1B-386C-8515-0CC182A63B5A> /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib
--- failed re-building ‘scDiagnostics.Rmd’

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

Error: Vignette re-building failed.
Execution halted