* using log directory 'd:/RCompile/CRANincoming/R-devel/MetabolSSMF.Rcheck'
* using R Under development (unstable) (2025-02-08 r87709 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 ... 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 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 ... [104s] ERROR
Running examples in 'MetabolSSMF-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gap
> ### Title: Gap statistic algorithm.
> ### Aliases: gap
> 
> ### ** Examples
> 
> # example code
> data <- SimulatedDataset
> 
> k <- 6
> 
> rss <- rep(NA, k)
> for(i in 1:k){
+   rss[i] <- ssmf(data = data, k = i)$SSE
+ }
> 
> gap(data = data, rss = rss)
$gap
[1] 0.7388749 1.1438675 1.5596871 1.8810473 1.8832631 1.8871320

$optimal.k
[1] 4

$standard.error
[1] 0.07354784 0.05642493 0.04443189 0.04477771 0.05655697 0.07266667

> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("gap", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
Error: connections left open:
	<-CRANwin3.fb05.statistik.uni-dortmund.de:11957 (sockconn)
	<-CRANwin3.fb05.statistik.uni-dortmund.de:11957 (sockconn)
Execution halted
Examples with CPU (user + system) or elapsed time > 10s
    user system elapsed
gap 2.17   0.41  102.06
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [11m] OK
* checking PDF version of manual ... [12s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 3 NOTEs