* using log directory ‘/srv/hornik/tmp/CRAN_pretest/holobiont.Rcheck’
* using R Under development (unstable) (2025-07-01 r88373)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3)
    Debian flang-new version 19.1.7 (3)
* running under: Debian GNU/Linux 13 (trixie)
* using session charset: UTF-8
* checking for file ‘holobiont/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘holobiont’ version ‘0.1.2’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/5s] WARNING
Maintainer: ‘Sharon Bewick <sbewick@clemson.edu>’

Insufficient package version (submitted: 0.1.2, existing: 0.1.2)

Suggests or Enhances not in mainstream repositories:
  microViz
Availability using Additional_repositories specification:
  microViz   no   ?                                          
  ?           ?   https://david-barnett.r-universe.dev/builds
Additional repositories with no packages:
  https://david-barnett.r-universe.dev/builds
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘microViz’
* 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 serialization versions ... OK
* checking whether package ‘holobiont’ can be installed ... [14s/14s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [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 ... [19s/19s] NOTE
basic_branch: no visible binding for global variable ‘seq_root2tip’
coreEdges: no visible global function definition for ‘phy_tree<-’
coreFaithsPD: no visible global function definition for ‘phy_tree<-’
corePhyloVenn: no visible global function definition for ‘phy_tree<-’
coreTree: no visible global function definition for ‘phy_tree<-’
coreUniFrac: no visible global function definition for ‘phy_tree<-’
coreVennTree: no visible global function definition for ‘phy_tree<-’
shade_branch: no visible binding for global variable ‘seq_root2tip’
Undefined global functions or variables:
  phy_tree<- seq_root2tip
* checking Rd files ... [0s/0s] 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 examples ... [40s/40s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
shade_branch 12.253  0.156  12.416
shade_np      6.620  0.000   6.625
shade_tip     6.569  0.008   6.580
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 WARNING, 2 NOTEs