* using log directory 'd:/RCompile/CRANincoming/R-devel/NicheBarcoding.Rcheck'
* using R Under development (unstable) (2024-08-29 r87078 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 'NicheBarcoding/DESCRIPTION' ... OK
* this is package 'NicheBarcoding' version '0.0.1.8000'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... WARNING
Maintainer: 'Cai-qing Yang <yangcq@cnu.edu.cn>'

Insufficient package version (submitted: 0.0.1.8000, existing: 1.0)
Version contains large components (0.0.1.8000)

New maintainer:
  Cai-qing Yang <yangcq@cnu.edu.cn>
Old maintainer(s):
  Cai-qing YANG <yangcq_ivy@163.com>

Possibly misspelled words in DESCRIPTION:
  barcodes (7:47)

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

DESCRIPTION fields with placeholder content:
  Title: what the package does (one line, title case)

Size of tarball: 10858424 bytes
* 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 serialization versions ... OK
* checking whether package 'NicheBarcoding' can be installed ... WARNING
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/RCompile/CRANincoming/R-devel/NicheBarcoding.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* checking installed package size ... 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:
  'LICENSE.md'
* 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 ... WARNING
'::' or ':::' import not declared from: 'car'
* 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 ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Variables with usage in Rd file 'LappetMoths.Rd' but not in code:
  'LappetMoths'

Variables with usage in Rd file 'bak.vir.Rd' but not in code:
  'bak.vir'

Variables with usage in Rd file 'en.vir.Rd' but not in code:
  'en.vir'

* checking Rd \usage sections ... OK
* 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 data for ASCII and uncompressed saves ... WARNING
  Warning: package needs dependence on R (>= 2.10)
* checking files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'NBSI.Rmd' 'how-to-do-stuff-NBSI.Rmd' 'how_it_works.Rmd'
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... ERROR
Running examples in 'NicheBarcoding-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: NBSI
> ### Title: Niche-model-Based Species Identification (NBSI)
> ### Aliases: NBSI
> ### Keywords: NBSI
> 
> ### ** Examples
> 
> data(en.vir)
> data(bak.vir)
> #envir<-raster::getData("worldclim",download=FALSE,var="bio",res=2.5)
> #en.vir<-raster::brick(envir)
> #back<-dismo::randomPoints(mask=en.vir,n=5000,ext=NULL,extf=1.1,
> #                          excludep=TRUE,prob=FALSE,
> #                          cellnumbers=FALSE,tryf=3,warn=2,
> #                          lonlatCorrection=TRUE)
> #bak.vir<-raster::extract(en.vir,back)
> 
> library(ape)
> data(LappetMoths)
> ref.seq<-LappetMoths$ref.seq[1:50,]
> que.seq<-LappetMoths$que.seq[1:5,]
> NBSI.out<-NBSI(ref.seq,que.seq,ref.add=NULL,
+                model="RF",en.vir=en.vir,bak.vir=bak.vir)
Error in loadNamespace(x) : there is no package called 'car'
Calls: NBSI ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in 'tests' ... WARNING
'library' or 'require' call not declared from: 'testthat'
* checking tests ... ERROR
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
* checking package vignettes ... NOTE
Package has 'vignettes' subdirectory but apparently no vignettes.
Perhaps the 'VignetteBuilder' information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... [14s] OK
* checking HTML version of manual ... OK
* DONE
Status: 2 ERRORs, 7 WARNINGs, 2 NOTEs