* 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 ’ Found the following (possibly) invalid URLs: URL: https://hgic.clemson.edu/factsheet/frequently-asked-questions-about-honey-bee-swarms (moved to https://hgic.clemson.edu/factsheet/frequently-asked-questions-about-honey-bee-swarms/) From: inst/doc/C_Colony_events.html 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. Found the following (possibly) invalid DOIs: DOI: /10.1007/bf00224018 From: man/calcBeeGRMIbd.Rd Status: 404 Message: Not Found DOI: /10.1007/bf00305821 From: man/calcBeeGRMIbd.Rd Status: 404 Message: Not Found DOI: /10.1017/s0016672310000480 From: man/calcBeeGRMIbd.Rd Status: 404 Message: Not Found DOI: /10.1038/nature14649 From: man/simulateHoneyBeeGenomes.Rd Status: 404 Message: Not Found DOI: /10.1038/ng.3077 From: man/simulateHoneyBeeGenomes.Rd Status: 404 Message: Not Found DOI: /10.1038/s41437-021-00411-2 From: man/calcInheritanceCriterion.Rd man/calcPerformanceCriterion.Rd man/calcSelectionCriterion.Rd Status: 404 Message: Not Found DOI: /10.1038/s41598-017-02629-9 From: man/SimParamBee.Rd Status: 404 Message: Not Found DOI: /10.1093/genetics/137.1.319 From: man/calcBeeGRMIbd.Rd Status: 404 Message: Not Found DOI: /10.1093/molbev/mst207 From: man/SimParamBee.Rd Status: 404 Message: Not Found DOI: /10.1093/oxfordjournals.jhered.a110812 From: man/calcBeeGRMIbd.Rd Status: 404 Message: Not Found DOI: /10.1101/gr.5680406 From: man/simulateHoneyBeeGenomes.Rd Status: 404 Message: Not Found DOI: /10.1186/s12711-020-00570-6 From: man/calcBeeGRMIbs.Rd Status: 404 Message: Not Found DOI: /10.1186/s12864-019-5642-0 From: man/simulateHoneyBeeGenomes.Rd Status: 404 Message: Not Found DOI: /10.1515/9780691189383 From: man/SimParamBee.Rd Status: 404 Message: Not Found DOI: /10.3390/insects12100868 From: man/SimParamBee.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 ... [14s/14s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [7s/7s] OK Running ‘testthat.R’ [6s/6s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [28s/28s] 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