* using log directory 'd:/RCompile/CRANincoming/R-devel/MetabolSSMF.Rcheck'
* using R Under development (unstable) (2025-01-22 r87618 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'MetabolSSMF/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MetabolSSMF' version '0.1.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Wenxuan Liu <wenxuan.liu@ucdconnect.ie>'

New submission

Possibly misspelled words in DESCRIPTION:
  Metabolomic (3:52)
  Metabolomics (16:50)
* 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 serialization versions ... OK
* checking whether package 'MetabolSSMF' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  'LICENSE.md'
* 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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 line widths ... NOTE
Rd file 'diversity.Rd':
  \examples lines wider than 100 characters:
     membership2 <- matrix(c(0.1, 0.2, 0.3, 0.4, 0.3, 0.2, 0.4, 0.1, 0.2, 0.3, 0.1, 0.4), nrow=3, ncol=4, byrow=TRUE)

These lines will be truncated in the PDF manual.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'MetabolSSMF.pdf' from 678Kb to 540Kb
  consider running tools::compactPDF() on these files,
  or build the source package with --compact-vignettes
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'MetabolSSMF-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bootstrap
> ### Title: Bootstrap algorithm function.
> ### Aliases: bootstrap
> 
> ### ** Examples
> 
> # example code
> data <- SimulatedDataset
> 
> k <- 4
> 
> fit <- ssmf(data = data, k = k)
> 
> bootstrap(data = data , k = k, H = fit$H)
Error in .check_ncores(length(names)) : 3 simultaneous processes spawned
Calls: bootstrap ... registerDoParallel -> makeCluster -> makePSOCKcluster -> .check_ncores
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [13s] ERROR
Error(s) in re-building vignettes:
--- re-building 'MetabolSSMF.Rmd' using rmarkdown

Quitting from lines 117-126 [unnamed-chunk-8] (MetabolSSMF.Rmd)
Error: processing vignette 'MetabolSSMF.Rmd' failed with diagnostics:
3 simultaneous processes spawned
--- failed re-building 'MetabolSSMF.Rmd'

SUMMARY: processing the following file failed:
  'MetabolSSMF.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [12s] OK
* checking HTML version of manual ... OK
* DONE
Status: 2 ERRORs, 4 NOTEs