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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ExperimentSubset.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ExperimentSubset_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/ExperimentSubset.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ExperimentSubset/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ExperimentSubset’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ExperimentSubset’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ExperimentSubset-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: reducedDimNames<-
> ### Title: reducedDimNames<-
> ### Aliases: reducedDimNames<- reducedDimNames<-,ANY-method
> 
> ### ** Examples
> 
> data(sce_chcl, package = "scds")
> es <- ExperimentSubset(sce_chcl)
> es <- createSubset(es, "subset1",
+ rows = c(1:1500), cols = c(1:1500),
+ parentAssay = "counts")
> reducedDims(es, subsetName = "subset1") <- list(
+ PCA_1 = scater::calculatePCA(assay(es, "subset1")),
+ PCA_2 = scater::calculatePCA(assay(es, "subset1")))
Error in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE,  : 
  function 'as_cholmod_sparse' not provided by package 'Matrix'
Calls: <Anonymous> ... runSVD -> do.call -> <Anonymous> -> do.call -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    4.     ├─BiocSingular::runPCA(...)
    5.     └─BiocSingular::runPCA(...)
    6.       └─BiocSingular (local) .local(x, ...)
    7.         ├─BiocSingular::runSVD(...)
    8.         └─BiocSingular::runSVD(...)
    9.           ├─BiocSingular::runSVD(...)
   10.           └─BiocSingular::runSVD(...)
   11.             ├─base::do.call(...)
   12.             └─BiocSingular (local) `<fn>`(...)
   13.               ├─base::do.call(...)
   14.               └─irlba (local) `<fn>`(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 118 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/ExperimentSubset.Rcheck/00check.log’
for details.