* using log directory ‘/srv/hornik/tmp/CRAN_pretest/CNSigs.Rcheck’
* using R Under development (unstable) (2025-11-23 r89052)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.5 (1)
    Debian flang version 21.1.5 (1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘CNSigs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNSigs’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Shawn Striker <striker.35@osu.edu>’

New submission

The Description field should not start with the package name,
  'This package' or similar.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘createSigs.Rd’:
    \keyword{signatures,}
  File ‘determineNumSigs.Rd’:
    \keyword{signatures,}
  File ‘extractCNFeats.Rd’:
    \keyword{bp10MB,}
    \keyword{bpchrarm,}
    \keyword{features,}
    \keyword{osCN,}
    \keyword{segsize,}
  File ‘findExposures.Rd’:
    \keyword{fixed,}
    \keyword{signatures,}
  File ‘fitModels.Rd’:
    \keyword{mixed,}
    \keyword{models,}
  File ‘generateSCM.Rd’:
    \keyword{matrix,}
  File ‘plotComp.Rd’:
    \keyword{component,}
  File ‘plotComps.Rd’:
    \keyword{component,}
  File ‘plotScm.Rd’:
    \keyword{plot,}
    \keyword{scm,}
  File ‘plotSegs.Rd’:
    \keyword{plot,}
  File ‘plotSig.Rd’:
    \keyword{plot,}
  File ‘plotSigExposure.Rd’:
    \keyword{sigExposure,}
  File ‘plotSigExposureMat.Rd’:
    \keyword{exposure,}
    \keyword{plot,}
    \keyword{sigExposure,}
    \keyword{signature,}
  File ‘plotSigMat.Rd’:
    \keyword{plot,}
    \keyword{signature,}
  File ‘plotSigs.Rd’:
    \keyword{signatures,}
  File ‘segStats.Rd’:
    \keyword{statistics,}
    \keyword{stats,}
  File ‘sigExprCor.Rd’:
    \keyword{exposure,}
    \keyword{expression,}
    \keyword{signature,}
  File ‘sigMutCor.Rd’:
    \keyword{exposure,}
    \keyword{mutation,}
    \keyword{signature,}
  File ‘validateSegData.Rd’:
    \keyword{validate,}
* 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 ‘CNSigs’ can be installed ... [7s/6s] 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 ... [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/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [10s/10s] OK
* checking Rd files ... [0s/0s] 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 ... [1s/1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/23s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [12s/20s] OK
* checking PDF version of manual ... [4s/4s] 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: 2 NOTEs