* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘polyRAD’ ...
** package ‘polyRAD’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/tmp/Rtmp6pCoLW/R.INSTALL94fee368dc0aa/polyRAD/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c AdjustAlleleFreq.cpp -o AdjustAlleleFreq.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c BestGenos.cpp -o BestGenos.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c FormatStructure.cpp -o FormatStructure.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GiniSimpson.cpp -o GiniSimpson.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c InitHapAssign.cpp -o InitHapAssign.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c PrepVCFexport.cpp -o PrepVCFexport.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c SimulateGenotypes.cpp -o SimulateGenotypes.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ThirdDimProd.cpp -o ThirdDimProd.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o polyRAD.so AdjustAlleleFreq.o BestGenos.o FormatStructure.o GiniSimpson.o InitHapAssign.o PrepVCFexport.o RcppExports.o SimulateGenotypes.o ThirdDimProd.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmp6pCoLW/R.INSTALL94fee368dc0aa/polyRAD/src'
make[1]: Entering directory '/tmp/Rtmp6pCoLW/R.INSTALL94fee368dc0aa/polyRAD/src'
make[1]: Leaving directory '/tmp/Rtmp6pCoLW/R.INSTALL94fee368dc0aa/polyRAD/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-polyRAD/00new/polyRAD/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘polyRAD’
    finding HTML links ... done
    AddAlleleFreqByTaxa                     html  
    AddAlleleFreqHWE                        html  
    AddAlleleFreqMapping                    html  
    AddAlleleLinkages                       html  
    AddGenotypeLikelihood                   html  
    AddGenotypePosteriorProb                html  
    AddGenotypePriorProb_ByTaxa             html  
    AddGenotypePriorProb_Even               html  
    AddGenotypePriorProb_HWE                html  
    AddGenotypePriorProb_Mapping2Parents    html  
    AddPCA                                  html  
    AddPloidyChiSq                          html  
    AddPloidyLikelihood                     html  
    CanDoGetWeightedMeanGeno                html  
    EstimateContaminationRate               html  
    ExamineGenotype                         html  
    ExpectedHindHe                          html  
    ExportGAPIT                             html  
    GetLikelyGen                            html  
    GetTaxa                                 html  
    GetWeightedMeanGenotypes                html  
    HindHe                                  html  
    InbreedingFromHindHe                    html  
    IterateHWE                              html  
    LocusInfo                               html  
    MakeTasselVcfFilter                     html  
    MergeIdenticalHaplotypes                html  
    MergeRareHaplotypes                     html  
    MergeTaxaDepth                          html  
    OneAllelePerMarker                      html  
    PipelineMapping2Parents                 html  
    RADdata                                 html  
    RADdata2VCF                             html  
    SetBlankTaxa                            html  
    StripDown                               html  
    SubsetByLocus                           html  
    SubsetByPloidy                          html  
    SubsetByTaxon                           html  
    TestOverdispersion                      html  
    VCF2RADdata                             html  
    exampleRAD                              html  
    readDArTag                              html  
    readHMC                                 html  
    readProcessIsoloci                      html  
    readProcessSamMulti                     html  
    readStacks                              html  
    readTASSELGBSv2                         html  
    readTagDigger                           html  
    reverseComplement                       html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (polyRAD)