* using log directory ‘/srv/hornik/tmp/CRAN_pretest/ggpicrust2.Rcheck’
* using R Under development (unstable) (2025-12-18 r89199)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.6 (2)
    Debian flang version 21.1.6 (2)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘ggpicrust2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggpicrust2’ version ‘2.5.5’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [6s/7s] NOTE
Maintainer: ‘Chen Yang <cafferychen7850@gmail.com>’

Suggests or Enhances not in mainstream repositories:
  Maaslin2

Found the following (possibly) invalid URLs:
  URL: https://cafferyang.com/ggpicrust2/
    From: DESCRIPTION
    Status: 404
    Message: Not Found
  URL: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02655-5 (moved to https://link.springer.com/article/10.1186/s13059-022-02655-5)
    From: README.md
    Status: 301
    Message: Moved Permanently
  URL: https://twitter.com/CafferyYang (moved to https://x.com/CafferyYang)
    From: README.md
    Status: 301
    Message: Moved Permanently
  URL: https://twitter.com/intent/tweet?url=https%3A%2F%2Fgithub.com%2Fcafferychen777%2Fggpicrust2&text=Check%20out%20this%20awesome%20package%20on%20GitHub%21 (moved to https://x.com/intent/tweet?url=https%3A%2F%2Fgithub.com%2Fcafferychen777%2Fggpicrust2&text=Check%20out%20this%20awesome%20package%20on%20GitHub%21)
    From: README.md
    Status: 301
    Message: Moved Permanently
For content that is 'Moved Permanently', please change http to https,
add trailing slashes, or replace the old by the new URL.
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘Maaslin2’
* 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 whether package ‘ggpicrust2’ can be installed ... [9s/9s] 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking whether startup messages can be suppressed ... [1s/1s] 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] NOTE
create_gradient_colors: no visible global function definition for
  ‘colorRampPalette’
pathway_errorbar_table: no visible global function definition for
  ‘setNames’
pathway_heatmap: no visible global function definition for ‘cor’
pathway_heatmap: no visible global function definition for ‘as.dist’
pathway_heatmap: no visible global function definition for ‘dist’
pathway_heatmap: no visible global function definition for ‘hclust’
perform_lefser_analysis : <anonymous>: no visible global function
  definition for ‘wilcox.test’
Undefined global functions or variables:
  as.dist colorRampPalette cor dist hclust setNames wilcox.test
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "setNames",
             "wilcox.test")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'ko_to_go_reference.Rd':
  \examples lines wider than 100 characters:
     metabolism_terms <- ko_to_go_reference[grepl("metabolic", ko_to_go_reference$go_name, ignore.case = TRUE), ]

These lines will be truncated in the PDF manual.
* 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 ... [0s/0s] 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 ... [4s/4s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [1s/1s] OK
* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [2s/2s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 3 NOTEs