* using log directory 'd:/RCompile/CRANincoming/R-devel/evanverse.Rcheck'
* using R Under development (unstable) (2025-09-17 r88852 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 'evanverse/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'evanverse' version '0.3.2'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Evan Zhou <evanzhou.bio@gmail.com>'

New submission

Possibly misspelled words in DESCRIPTION:
  bioinformatics (12:60)

Found the following (possibly) invalid file URIs:
  URI: visualization-showcase.html
    From: inst/doc/bioinformatics-workflows.html
  URI: visualization-showcase.html
    From: inst/doc/color-palettes.html
  URI: visualization-showcase.html
    From: inst/doc/data-processing.html

Size of tarball: 6572736 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'evanverse' 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:
  'CRAN-submission-checklist.md' 'cran-comments.md'
  'cross-platform-compatibility-report.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 whether startup messages can be suppressed ... 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 ... [12s] NOTE
plot_density: no visible binding for global variable 'density'
Undefined global functions or variables:
  density
Consider adding
  importFrom("stats", "density")
to your NAMESPACE file.
* 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 ... WARNING
Variables with usage in Rd file 'df_forest_test.Rd' but not in code:
  'df_forest_test'

Variables with usage in Rd file 'trial.Rd' but not in code:
  'trial'

Codoc mismatches from Rd file 'grapes-nin-grapes.Rd':
%nin%
  Code: function(...)
  Docs: function(x, table)
  Argument names in code not in docs:
    ...
  Argument names in docs not in code:
    x table
  Mismatches in argument names:
    Position: 1 Code: ... Docs: x

* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'grapes-nin-grapes.Rd'
  'x' 'table'
Documented arguments not in \usage in Rd file 'grapes-nin-grapes.Rd':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [13s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [40s] OK
  Running 'testthat.R' [40s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [44s] OK
* checking PDF version of manual ... [22s] OK
* checking HTML version of manual ... OK
* DONE
Status: 2 WARNINGs, 3 NOTEs