- using R Under development (unstable) (2024-07-24 r86924)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-13 (Debian 13.3.0-3) 13.3.0
GNU Fortran (Debian 13.3.0-3) 13.3.0
- 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 ‘0.3.0’
- 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 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 ... OK
See the install log for details.
- 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 ... [1s/1s] OK
- checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the package can be unloaded cleanly ... [1s/1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
- checking loading without being on the library search path ... [1s/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 ... [17s/30s] OK
- checking Rd files ... [1s/3s] 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 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
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 ... [24s/33s] OK
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [357s/266s] OK
- checking PDF version of manual ... [10s/18s] OK
- checking HTML version of manual ... [5s/10s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 NOTEs