* using log directory 'd:/RCompile/CRANincoming/R-devel/CATS.Rcheck'
* using R Under development (unstable) (2025-10-16 r88927 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'CATS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CATS' version '0.1.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... ERROR
Maintainer: 'Gulden Olgun <gulden@cs.bilkent.edu.tr>'

New submission

Conflicting package names (submitted: CATS, existing: cats [https://bioconductor.statistik.tu-dortmund.de/cran])

Possibly misspelled words in DESCRIPTION:
  PPI (8:814)
  Transcriptomic (3:24, 8:415)
  geneset (8:507, 8:588, 8:799, 8:869)
  stemness (8:174)
  transcriptomic (8:272)
  upregulation (8:936)

Found the following URLs which should use \doi (with the DOI name only):
  File 'human_PPIN.Rd':
    https://doi.org/10.1038/s41540-017-0005-4
* 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 whether package 'CATS' 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 ... 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 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 ... [33s] 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [34m] NOTE
Examples with CPU (user + system) or elapsed time > 10s
                           user system elapsed
ContextSpecificExpansion 521.89 161.94  684.39
runCATS                  523.13 146.83  670.03
getDEgenes               525.06 140.98  666.62
getCorr                   20.89   0.70   21.59
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... OK
  Running 'testthat.R'
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [23m] OK
* checking PDF version of manual ... [19s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE