* using log directory ‘/srv/hornik/tmp/CRAN_pretest/BAZE.Rcheck’
* using R Under development (unstable) (2025-10-15 r88920)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (7)
    Debian flang-new version 19.1.7 (7)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘BAZE/DESCRIPTION’ ... OK
* this is package ‘BAZE’ version ‘1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Ruitao Liu <rxl761@case.edu>’

New submission

Possibly misspelled words in DESCRIPTION:
  Liangliang (9:14)
  Microbiome (2:41)
  Zhang's (9:25)
  microbiome (7:61)

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ruitao",
                    family = "Liu",
                    role = c("aut", "cre"),
                    email = "rxl761@case.edu")
as necessary.
* 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 whether package ‘BAZE’ can be installed ... [15s/15s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘BAZE.Rproj’
* 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 ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
* checking loading without being on the library search path ... [4s/4s] 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 ... [20s/20s] NOTE
detailed_tax: no visible binding for global variable ‘node’
detailed_tax: no visible binding for global variable ‘label’
detailed_tax: no visible binding for global variable ‘x’
detailed_tax: no visible binding for global variable ‘y’
detailed_tax: no visible binding for global variable ‘annot’
effect_plot: no visible binding for global variable ‘Sign’
effect_sign: no visible binding for global variable ‘node’
get_selected_id: no visible binding for global variable ‘.’
phy_to_tax: no visible binding for global variable ‘value’
plottax : plottree: no visible binding for global variable ‘nodeSize’
plottax: no visible binding for global variable ‘node’
plottax: no visible binding for global variable ‘label’
plottax: no visible binding for global variable ‘nodeSize’
plottax: no visible binding for global variable ‘x’
plottax: no visible binding for global variable ‘y’
plottax: no visible binding for global variable ‘annot’
summarize_taxa: no visible binding for global variable ‘sample_id’
summarize_taxa: no visible binding for global variable ‘value’
tax_rel : plottree: no visible binding for global variable ‘nodeSize’
tax_rel: no visible binding for global variable ‘label’
tax_rel: no visible binding for global variable ‘isTip’
tax_rel: no visible binding for global variable ‘phylum’
tax_rel: no visible binding for global variable ‘nodeSize’
tax_rel: no visible binding for global variable ‘annot’
tax_rel: no visible binding for global variable ‘taxaAbun’
tax_rel: no visible binding for global variable ‘xstart’
tax_rel: no visible binding for global variable ‘xend’
tax_rel: no visible binding for global variable ‘y’
taxview: no visible binding for global variable ‘Size’
Undefined global functions or variables:
  . Sign Size annot isTip label node nodeSize phylum sample_id taxaAbun
  value x xend xstart y
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'detailed_tax.Rd':
  \examples lines wider than 100 characters:
     anno.data <- data.frame(node = c("node1", "node2"), color = c("red", "blue"))  # Replace with actual annotation data

Rd file 'get_selected_id.Rd':
  \examples lines wider than 100 characters:
     anno.data <- data.frame(node = c("g__Bacteroides", "f__Lachnospiraceae"), color = c("red", "blue"))  # Replace with actual annotation d ... [TRUNCATED]

Rd file 'tax_rel.Rd':
  \examples lines wider than 100 characters:
     p <- tax_rel(tree, anno.data, alpha = 0.2, anno.depth = 3, anno.x = 10, anno.y = 40, scale_size = 0.5)

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 examples ... [8s/8s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [5s/5s] OK
  Running ‘testthat.R’ [4s/4s]
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 4 NOTEs