* using log directory ‘/srv/hornik/tmp/CRAN/SIMplyBee.Rcheck’
* using R Under development (unstable) (2024-08-22 r87039)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (9)
    Debian flang-new version 18.1.8 (9)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘SIMplyBee/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIMplyBee’ version ‘0.4.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/8s] NOTE
Maintainer: ‘Jana Obšteter <obsteter.jana@gmail.com>’

Found the following (possibly) invalid DOIs:
  DOI: 0.1038/ng.3077
    From: man/simulateHoneyBeeGenomes.Rd
    Status: 400
    Message: Bad Request
  DOI: doi.org/10.1038/nature14649
    From: man/simulateHoneyBeeGenomes.Rd
    Status: 404
    Message: Not Found
* 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 serialization versions ... OK
* checking whether package ‘SIMplyBee’ can be installed ... [12s/12s] OK
* used C++ compiler: ‘Debian clang version 18.1.8 (9)’
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [8s/8s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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
  createCrossPlan.Rd: Pop-class
  createDCA.Rd: Pop-class
  createMatingStationDCA.Rd: Pop-class
  createMultiColony.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
  getMisc.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
  setMisc.Rd: Pop-class
  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 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/13s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [6s/6s] OK
  Running ‘testthat.R’ [6s/6s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [27s/27s] OK
* checking PDF version of manual ... [5s/5s] OK
* checking HTML version of manual ... [2s/2s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 NOTEs