* using log directory ‘/srv/hornik/tmp/CRAN/S2IsoMEr.Rcheck’
* using R Under development (unstable) (2024-08-19 r87028)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (9)
    Debian flang-new version 18.1.8 (9)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘S2IsoMEr/DESCRIPTION’ ... OK
* this is package ‘S2IsoMEr’ version ‘0.4.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/9s] NOTE
Maintainer: ‘Bishoy Wadie <bishoy.wadie@embl.de>’

New submission

Possibly misspelled words in DESCRIPTION:
  MSEA (13:109)
  Overrepresentation (13:35)
  metabolomics (13:142)

Found the following (possibly) invalid URLs:
  URL: https://academic.oup.com/bioinformatics/article/39/1/btac726/6827287
    From: README.md
    Status: 403
    Message: Forbidden
  URL: https://academic.oup.com/bioinformaticsadvances/article/2/1/vbac016/6544613
    From: man/decouple_ORA_wrapper.Rd
    Status: 403
    Message: Forbidden
  URL: https://academic.oup.com/nar/article/38/suppl_2/W71/1101310
    From: inst/doc/MSEA_enrichment-single_cell_metabolomics.html
    Status: 403
    Message: Forbidden

Size of tarball: 37953679 bytes
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘S2IsoMEr’ can be installed ... [263s/263s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [29s/29s] NOTE
Run_bootstrap_MSEA : <anonymous> : <anonymous>: no visible global
  function definition for ‘ks.test.2’
Run_simple_MSEA : <anonymous>: no visible global function definition
  for ‘ks.test.2’
ridge_bootstraps: no visible binding for global variable ‘density’
Undefined global functions or variables:
  density ks.test.2
Consider adding
  importFrom("stats", "density")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] NOTE
checkRd: (-1) Load_background.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Load_background.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Load_background.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Load_background.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Load_background.Rd:22: Lost braces in \itemize; meant \describe ?
* 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 ... [2s/2s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/2s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [2s/2s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 3 NOTEs