* 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++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpUtXeL1/R.INSTALL252dc449cc098b/polyRAD/src'
g++-14 -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++-14 -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++-14 -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++-14 -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++-14 -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++-14 -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++-14 -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++-14 -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++-14 -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++-14 -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 '/home/hornik/tmp/scratch/RtmpUtXeL1/R.INSTALL252dc449cc098b/polyRAD/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpUtXeL1/R.INSTALL252dc449cc098b/polyRAD/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpUtXeL1/R.INSTALL252dc449cc098b/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)