* using log directory 'd:/RCompile/CRANincoming/R-devel/ggpicrust2.Rcheck'
* using R Under development (unstable) (2024-10-11 r87226 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'ggpicrust2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ggpicrust2' version '1.7.3'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [51s] WARNING
Maintainer: 'Chen Yang <cafferychen7850@gmail.com>'

Insufficient package version (submitted: 1.7.3, existing: 1.7.3)

Found the following (possibly) invalid URLs:
  URL: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad470/7234609?utm_source=advanceaccess&utm_campaign=bioinformatics&utm_medium=email&login=false
    From: README.md
    Status: 403
    Message: Forbidden
  URL: https://bioconductor.riken.jp/packages/3.9/bioc/html/ALDEx2.html
    From: inst/doc/using_ggpicrust2.html
    Status: Error
    Message: Failed to connect to bioconductor.riken.jp port 443 after 21044 ms: Couldn't connect to server
  URL: https://opensource.org/license/mit/ (moved to https://opensource.org/license/mit)
    From: inst/doc/using_ggpicrust2.html
          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 ... 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 'ggpicrust2' 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'pathway_heatmap.Rd':
  \examples lines wider than 100 characters:
                                           metadata = metadata, group = "Environment", daa_method = "LinDA")
                                                            daa_results_df = metacyc_daa_results_df, ko_to_kegg = FALSE)
                                select(all_of(c("feature","description"))), by = c("pathway" = "feature")) %>%

Rd file 'pathway_pca.Rd':
  \examples lines wider than 100 characters:
     pathway_pca(metacyc_abundance %>% column_to_rownames("pathway"), metadata, "Environment", colors = c("green", "purple"))

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 ... WARNING
Undocumented arguments in Rd file 'pathway_pca.Rd'
  'colors'

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 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 ... 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: 2 WARNINGs, 1 NOTE