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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scDesign3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scDesign3_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scDesign3.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scDesign3/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scDesign3’ version ‘1.4.0’
* 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 ‘scDesign3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘scDesign3-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: perform_lrt
> ### Title: Perform the likelihood ratio test
> ### Aliases: perform_lrt
> 
> ### ** Examples
> 
> data(example_sce)
> my_data <- construct_data(
+ sce = example_sce,
+ assay_use = "counts",
+ celltype = "cell_type",
+ pseudotime = "pseudotime",
+ spatial = NULL,
+ other_covariates = NULL,
+ corr_by = "cell_type"
+ )
> 
> my_data2 <- construct_data(
+   sce = example_sce,
+   assay_use = "counts",
+   celltype = "cell_type",
+   pseudotime = "pseudotime",
+   spatial = NULL,
+   other_covariates = NULL,
+   corr_by = "pseudotime",
+   ncell = 10000
+ )
Warning in mclapply(seq_len(n), do_one, mc.preschedule = mc.preschedule,  :
  all scheduled cores encountered errors in user code
Error in dimnames(x) <- dn : 
  length of 'dimnames' [1] not equal to array extent
Calls: construct_data -> as.data.frame -> simuCovariateMat -> rownames<-
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:
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-scDesign3.R:16:3'): Run scDesign3 ──────────────────────────────
  Error in `dimnames(x) <- dn`: length of 'dimnames' [1] not equal to array extent
  Backtrace:
      ▆
   1. └─scDesign3::construct_data(...) at test-scDesign3.R:16:3
   2.   ├─base::as.data.frame(...)
   3.   └─scDesign3:::simuCovariateMat(dat, ncell, parallelization, BPPARAM)
   4.     └─base::`rownames<-`(`*tmp*`, value = paste0("Cell", seq_len(n_cell_new)))
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/scDesign3.Rcheck/00check.log’
for details.