* using log directory ‘/srv/hornik/tmp/CRAN/pbgeno.Rcheck’
* using R Under development (unstable) (2023-11-23 r85618)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.5 (1)
    Debian flang-new version 17.0.5 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘pbgeno/DESCRIPTION’ ... OK
* this is package ‘pbgeno’ version ‘0.0.0.9000’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Allan Victor <albertoogy@gmail.com>’

New submission

Version contains large components (0.0.0.9000)

The Title field should be in title case. Current version is:
‘This package is for plant breeding data analysis, provides publication-ready tables and beautiful figures without writing a lot of code in R’
In title case that is:
‘This Package is for Plant Breeding Data Analysis, Provides Publication-Ready Tables and Beautiful Figures without Writing a Lot of Code in R’

The Description field should not start with the package name,
  'This package' or similar.
* 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 serialization versions ... OK
* checking whether package ‘pbgeno’ can be installed ... [1s/1s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
License components which are templates and need '+ file LICENSE':
  MIT License
Authors@R field gives no person with name and author role
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' calls not declared from:
  ‘RColorBrewer’ ‘ape’ ‘cluster’ ‘factoextra’ ‘ggplot2’ ‘ggtree’
  ‘ggtreeExtra’ ‘gt’ ‘tidyr’
'library' or 'require' calls in package code:
  ‘RColorBrewer’ ‘ape’ ‘cluster’ ‘factoextra’ ‘ggplot2’ ‘ggtree’
  ‘ggtreeExtra’ ‘gt’ ‘tidyr’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [2s/2s] NOTE
ggtree_jaccard: no visible global function definition for ‘%>%’
ggtree_jaccard: no visible global function definition for ‘gt’
ggtree_jaccard: no visible global function definition for ‘tab_header’
ggtree_jaccard: no visible global function definition for ‘md’
ggtree_jaccard: no visible global function definition for
  ‘tab_source_note’
ggtree_jaccard: no visible global function definition for ‘tab_options’
ggtree_jaccard: no visible global function definition for ‘px’
ggtree_jaccard: no visible global function definition for ‘opt_stylize’
ggtree_jaccard: no visible global function definition for ‘pct’
ggtree_jaccard: no visible global function definition for ‘as.dist’
ggtree_jaccard: no visible global function definition for ‘hclust’
ggtree_jaccard: no visible global function definition for ‘cutree’
ggtree_jaccard: no visible global function definition for ‘as.phylo’
ggtree_jaccard: no visible global function definition for ‘ggtree’
ggtree_jaccard: no visible global function definition for
  ‘geom_tippoint’
ggtree_jaccard: no visible global function definition for ‘aes’
ggtree_jaccard: no visible binding for global variable ‘Clusters’
ggtree_jaccard: no visible global function definition for ‘geom_tiplab’
pic_calc : pic_multi: no visible global function definition for ‘combn’
str2tassel: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  %>% Clusters aes as.dist as.phylo combn cutree geom_tiplab
  geom_tippoint ggtree gt hclust md na.omit opt_stylize pct px
  tab_header tab_options tab_source_note
Consider adding
  importFrom("stats", "as.dist", "cutree", "hclust", "na.omit")
  importFrom("utils", "combn")
to your NAMESPACE file.
* 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 ... WARNING
Undocumented arguments in Rd file 'ggtree_jaccard.Rd'
  ‘nclust_jaccard’ ‘offset_label’
Documented arguments not in \usage in Rd file 'ggtree_jaccard.Rd':
  ‘`nclust_jaccard`’ ‘`offset_label`’

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 ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [1s/1s] ERROR
Running examples in ‘pbgeno-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: str2tassel
> ### Title: Convert STRUCTURE format data to TASSEL format
> ### Aliases: str2tassel
> 
> ### ** Examples
> 
>  
> data(Structure_example)
> tassel_data <- str2tassel(data=Structure_example,met=metadata,na.strings="-9")
> write.table(tassel_data,"Tassel_hapmap.txt", row.names = F,quote = F, sep = "\t")
Error in write.table(tassel_data, "Tassel_hapmap.txt", row.names = F,  : 
  F used instead of FALSE
Execution halted
* checking PDF version of manual ... [2s/2s] 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: 1 ERROR, 2 WARNINGs, 4 NOTEs