* using log directory ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/MARVEL.Rcheck’
* using R Under development (unstable) (2025-01-24 r87627)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.3.1
* using session charset: UTF-8
* checking for file ‘MARVEL/DESCRIPTION’ ... OK
* this is package ‘MARVEL’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Packages suggested but not available for checking:
  'BSgenome', 'BSgenome.Hsapiens.NCBI.GRCh38', 'factoextra',
  'FactoMineR', 'org.Hs.eg.db', 'org.Mm.eg.db', 'wiggleplotr'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MARVEL’ can be installed ... [14s/22s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-macos-x86_64/MARVEL-00install.html' for details.
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/3s] OK
* checking loading without being on the library search path ... [2s/3s] 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 ... [21s/36s] OK
* checking Rd files ... [1s/1s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [31s/54s] ERROR
Running examples in ‘MARVEL-Ex.R’ failed
The error most likely occurred in:

> ### Name: RunPCA.Exp
> ### Title: Principle component analysis for gene Data
> ### Aliases: RunPCA.Exp
> 
> ### ** Examples
> 
> marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL"))
> 
> # Define genes for analysis
> gene_ids <- marvel.demo$Exp$gene_id
> 
> # PCA
> marvel.demo <- RunPCA.Exp(MarvelObject=marvel.demo,
+                           sample.ids=marvel.demo$SplicePheno$sample.id,
+                           cell.group.column="cell.type",
+                           cell.group.order=c("iPSC", "Endoderm"),
+                           min.cells=5,
+                           features=gene_ids,
+                           point.size=2
+                           )
Error in loadNamespace(x) : there is no package called ‘FactoMineR’
Calls: RunPCA.Exp ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [11s/20s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘MARVEL.Rmd’ using rmarkdown

Quitting from lines 60-71 [unnamed-chunk-4] (MARVEL.Rmd)
Error: processing vignette 'MARVEL.Rmd' failed with diagnostics:
there is no package called 'FactoMineR'
--- failed re-building ‘MARVEL.Rmd’

SUMMARY: processing the following file failed:
  ‘MARVEL.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [11s/19s] OK
* DONE
Status: 2 ERRORs
* using check arguments '--no-clean-on-error '

* elapsed time (check, wall clock): 3:47