* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘SimBIID’ ...
** package ‘SimBIID’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-12) 14.2.0’
using C++11
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpuoqPoV/R.INSTALL314b90292a9333/SimBIID/src'
g++-14 -std=gnu++11 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/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++11 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c adaptUpdate.cpp -o adaptUpdate.o
g++-14 -std=gnu++11 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c bootstrapParticleFilter.cpp -o bootstrapParticleFilter.o
g++-14 -std=gnu++11 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c bootstrapParticleFilterState.cpp -o bootstrapParticleFilterState.o
g++-14 -std=gnu++11 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c cholArma.cpp -o cholArma.o
g++-14 -std=gnu++11 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c mvrnormArma.cpp -o mvrnormArma.o
g++-14 -std=gnu++11 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c pmcmc.cpp -o pmcmc.o
g++-14 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o SimBIID.so RcppExports.o adaptUpdate.o bootstrapParticleFilter.o bootstrapParticleFilterState.o cholArma.o mvrnormArma.o pmcmc.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpuoqPoV/R.INSTALL314b90292a9333/SimBIID/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpuoqPoV/R.INSTALL314b90292a9333/SimBIID/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpuoqPoV/R.INSTALL314b90292a9333/SimBIID/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-SimBIID/00new/SimBIID/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘SimBIID’
    finding HTML links ... done
    ABCRef                                  html  
    ABCSMC                                  html  
    PMCMC                                   html  
    SimBIID-package                         html  
    compileRcpp                             html  
    ebola                                   html  
    mparseRcpp                              html  
    plot.ABCSMC                             html  
    plot.PMCMC                              html  
    plot.SimBIID_runs                       html  
    predict.PMCMC                           html  
    print.ABCSMC                            html  
    print.PMCMC                             html  
    print.SimBIID_model                     html  
    print.SimBIID_runs                      html  
    run                                     html  
    smallpox                                html  
    summary.ABCSMC                          html  
    summary.PMCMC                           html  
    window.PMCMC                            html  
    finding level-2 HTML links ... done

** building package indices
** 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 (SimBIID)