* using log directory 'd:/RCompile/CRANincoming/R-devel/qtlpoly.Rcheck'
* using R Under development (unstable) (2024-03-18 r86148 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 'qtlpoly/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'qtlpoly' version '0.2.4'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Gabriel de Siqueira Gesteira <gdesiqu@ncsu.edu>'

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  Autopolyploids (3:46)
  Pereira (37:212)
  QTL (3:31)
  REMIM (37:64)
  REML (37:157)
  al (37:223)
  autopolyploid (37:95)
  et (37:220)
  sib (37:79)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2024-03-19 as issues were not corrected
    in time.

Found the following (possibly) invalid URLs:
  URL: https://polyploids.r-universe.dev/ui#builds (moved to http://polyploids.r-universe.dev/ui/#builds)
    From: README.md
    Status: 301
    Message: Moved Permanently
  URL: https://www.bioss.ac.uk/knowledge/tetraploidmap/ (moved to https://www.bioss.ac.uk/knowledge-exchange/software/TetraploidSNPMap)
    From: README.md
    Status: 301
    Message: Moved Permanently
  URL: https://www.springer.com/gp/book/9780387981413 (moved to https://link.springer.com/book/10.1007/978-0-387-98141-3)
    From: README.md
    Status: 301
    Message: Moved Permanently
  For content that is 'Moved Permanently', please change http to https,
  add trailing slashes, or replace the old by the new URL.
* 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 'qtlpoly' can be installed ... OK
* used C++ compiler: 'g++.exe (GCC) 13.2.0'
* 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 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 ... OK
* checking S3 generic/method consistency ... NOTE
Mismatches for apparent methods not registered:
varComp.test:
  function(object, ...)
varComp.test.2modelDoTest:
  function(null.fit, alt.fit, test, control, ...)

varComp.test:
  function(object, ...)
varComp.test.nulDoTest:
  function(null.fit, additional.varcov, test, control, alt.fit, ...)

varComp.test:
  function(object, ...)
varComp.test.altDoTest:
  function(alt.fit, null, test, control, null.fit, ...)
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 ... [24s] 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 ... 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 LazyData ... 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 examples ... OK
* checking PDF version of manual ... [14s] OK
* checking HTML version of manual ... OK
* DONE
Status: 2 NOTEs