* using log directory 'd:/Rcompile/CRANpkg/local/4.5/SIMplyBee.Rcheck'
* using R Under development (unstable) (2024-07-14 r86899 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 'SIMplyBee/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SIMplyBee' version '0.3.0'
* package encoding: UTF-8
* 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 'SIMplyBee' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s] OK
* checking whether the package can be unloaded cleanly ... [1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s] OK
* checking loading without being on the library search path ... [1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [10s] OK
* checking Rd files ... [2s] NOTE
checkRd: (-1) cross.Rd:11: Lost braces
    11 | \item{x}{\code{\link{Pop-class}} or code{\link{Colony-class}} or \code{\link{MultiColony-class}},
       |                                         ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Colony-class.Rd: Pop-class
  SimParamBee.Rd: SimParam, MapPop-class
  calcInheritanceCriterion.Rd: Pop-class
  calcQueensPHomBrood.Rd: Pop-class
  combineBeeGametes.Rd: Pop-class
  combineBeeGametesHaploDiploid.Rd: Pop-class
  combineNULLAndPop.Rd: Pop-class
  createCastePop.Rd: Pop-class
  createColony.Rd: Pop-class
  createDCA.Rd: Pop-class
  createMatingStationDCA.Rd: Pop-class
  createMultiColony.Rd: Pop-class
  createRandomCrossPlan.Rd: Pop-class
  cross.Rd: Pop-class
  downsize.Rd: selectInd
  editCsdLocus.Rd: Pop-class
  getAa.Rd: Pop-class, dd
  getBv.Rd: Pop-class, bv
  getCaste.Rd: Pop-class
  getCasteId.Rd: Pop-class
  getCastePop.Rd: Pop-class, selectInd, mergePops
  getCasteSex.Rd: Pop-class
  getCsdAlleles.Rd: Pop-class
  getCsdGeno.Rd: Pop-class
  getDd.Rd: Pop-class, dd
  getGv.Rd: Pop-class, gv
  getIbdHaplo.Rd: Pop-class, pullIbdHaplo
  getId.Rd: Pop-class
  getPheno.Rd: Pop-class, pheno
  getQtlGeno.Rd: Pop-class, pullQtlGeno
  getQtlHaplo.Rd: Pop-class, pullQtlHaplo
  getQueenAge.Rd: Pop-class
  getQueenYearOfBirth.Rd: Pop-class
  getSegSiteGeno.Rd: Pop-class, pullSegSiteGeno
  getSegSiteHaplo.Rd: Pop-class, pullSegSiteHaplo
  getSnpGeno.Rd: Pop-class, pullSnpGeno
  getSnpHaplo.Rd: Pop-class, pullSnpHaplo
  isCaste.Rd: Pop-class
  isCsdHeterozygous.Rd: Pop-class
  isEmpty.Rd: Pop-class
  mapCasteToColonyValue.Rd: pheno, gv
  nCsdAlleles.Rd: Pop-class
  nDronesFun.Rd: Pop-class
  pullCastePop.Rd: selectInd, Pop-class
  pullDroneGroupsFromDCA.Rd: Pop-class
  pullInd.Rd: Pop-class, selectInd
  reQueen.Rd: Pop-class
  reduceDroneGeno.Rd: Pop-class
  reduceDroneHaplo.Rd: Pop-class
  removeCastePop.Rd: selectInd
  replaceCastePop.Rd: selectInd
  setQueensYearOfBirth.Rd: Pop-class
  simulateHoneyBeeGenomes.Rd: MapPop-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [16s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [285s] OK
* checking PDF version of manual ... [26s] OK
* checking HTML version of manual ... [18s] OK
* DONE
Status: 2 NOTEs