* using log directory 'd:/RCompile/CRANincoming/R-devel/graphsim.Rcheck'
* using R Under development (unstable) (2025-04-29 r88182 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 'graphsim/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'graphsim' version '1.0.4'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'S. Thomas Kelly <tomkellygenetics@gmail.com>'

Problems when reading CITATION file:
  no package 'graphsim' was found
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

The Date field is over a month old.
* 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 'graphsim' 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 files/directories found at top level:
  'CITATION.cff' 'cran-comments.md'
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Found the following CITATION file in a non-standard place:
  CITATION.cff
Most likely 'inst/CITATION' should be used instead.
* 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 ... NOTE
Mismatches for apparent methods not registered:
plot:
  function(x, ...)
plot.directed:
  function(graph, state, labels, layout, cex.node, cex.label,
           cex.arrow, cex.main, cex.sub, arrow_clip, pch, border.node,
           fill.node, col.label, col.arrow, main, sub, xlab, ylab,
           frame.plot)
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [10s] 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 ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [15s] OK
* checking HTML version of manual ... OK
* DONE
Status: 4 NOTEs