* using log directory ‘/srv/hornik/tmp/CRAN/geneHapR.Rcheck’
* using R Under development (unstable) (2024-02-28 r85999)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.6 (5)
    Debian flang-new version 17.0.6 (5)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘geneHapR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geneHapR’ version ‘1.2.3’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/6s] NOTE
Maintainer: ‘Zhang Renliang <zhang_renliang@163.com>’

New submission

Package was archived on CRAN

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2024-02-10 as check problems were not
    corrected in time
* 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 ‘geneHapR’ can be installed ... [25s/25s] 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... NOTE
Mismatches for apparent methods not registered:
wilcox.test:
  function(x, ...)
wilcox.test.ps:
  function(phenos)

t.test:
  function(x, ...)
t.test.ps:
  function(phenos)
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [36s/36s] NOTE
hapDistribution: no visible binding for global variable ‘china’
Undefined global functions or variables:
  china
* 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 ... WARNING
Undocumented code objects:
  ‘china’
Undocumented data sets:
  ‘china’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'import_hap.Rd':
import_hap
  Code: function(file, type = "auto", ...)
  Docs: function(file, ...)
  Argument names in code not in docs:
    type
  Mismatches in argument names:
    Position: 2 Code: type Docs: ...

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in Rd file 'import_hap.Rd':
  ‘type’

Undocumented arguments in Rd file 'plotHapTable2.Rd'
  ‘INFO_split’ ‘INFO_tag’ ‘geneID’ ‘tag_field’

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 ... [3s/3s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [27s/27s] ERROR
Running examples in ‘geneHapR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotHapTable2
> ### Title: plotHapTable2
> ### Aliases: plotHapTable2
> 
> ### ** Examples
> 
> #
> data(geneHapR_test)
> plotHapTable2(hapResult)
> plotHapTable2(hapResult, gff = gff)
Error: invalid subscript
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [7s/7s] OK
  Running ‘testthat.R’ [7s/7s]
* 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 ... [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 ERROR, 3 WARNINGs, 3 NOTEs