* using log directory 'd:/RCompile/CRANincoming/R-devel/QTLRel.Rcheck'
* using R Under development (unstable) (2023-08-05 r84874 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'QTLRel/DESCRIPTION' ... OK
* this is package 'QTLRel' version '1.13'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Riyan Cheng <riyancheng@hotmail.com>'

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.
* 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 whether package 'QTLRel' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used Fortran compiler: 'GNU Fortran (GCC) 12.2.0'
* checking installed package size ... 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 R 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 startup messages can be suppressed ... 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:
scanTwo:
  function(y, x, gdat, prdat, vc, numGeno, minorGenoFreq, rmv)
scanTwo.1:
  function(y, x, prdat, cov)

scanTwo:
  function(y, x, gdat, prdat, vc, numGeno, minorGenoFreq, rmv)
scanTwo.2:
  function(y, x, gdat, cov, numGeno)

scanOne:
  function(y, x, gdat, prdat, vc, intc, numGeno, test, minorGenoFreq,
           rmv)
scanOne.0:
  function(y, x, prdat, hinvCov, intc, test)

scanOne:
  function(y, x, gdat, prdat, vc, intc, numGeno, test, minorGenoFreq,
           rmv)
scanOne.1:
  function(y, x, prdat, hinvCov, intc, test)

scanOne:
  function(y, x, gdat, prdat, vc, intc, numGeno, test, minorGenoFreq,
           rmv)
scanOne.2:
  function(y, x, gdat, hinvCov, intc, numGeno, test)

plot:
  function(x, ...)
plot.lrt:
  function(lrt, cv, ...)

Apparent methods for exported generics not registered:
  scanOne.0 scanOne.1 scanOne.2 scanTwo.1 scanTwo.2
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 ... [12s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  '.lodci'
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 ... OK
* 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 ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs