* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘PAC’ ...
** package ‘PAC’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-23) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
using C++11
make[1]: Entering directory '/tmp/RtmpVCGM8e/R.INSTALL1405ac51e7c7a5/PAC/src'
g++-13 -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/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-13 -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/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c bsp.cc -o bsp.o
g++-13 -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/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c pac-wrapper.cc -o pac-wrapper.o
pac-wrapper.cc: In function ‘Rcpp::NumericMatrix BSPLeaveCenterCpp(Rcpp::NumericMatrix, SEXP, SEXP)’:
pac-wrapper.cc:69:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   69 |                 for(int j = 0; j < T.leafctr[0].size(); j++) {
      |                                ~~^~~~~~~~~~~~~~~~~~~~~
gcc-13 -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 -Wstrict-prototypes -pedantic -mtune=native  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++-13 -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/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c util.cc -o util.o
g++-13 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o PAC.so RcppExports.o bsp.o pac-wrapper.o registerDynamicSymbol.o util.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpVCGM8e/R.INSTALL1405ac51e7c7a5/PAC/src'
make[1]: Entering directory '/tmp/RtmpVCGM8e/R.INSTALL1405ac51e7c7a5/PAC/src'
make[1]: Leaving directory '/tmp/RtmpVCGM8e/R.INSTALL1405ac51e7c7a5/PAC/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-PAC/00new/PAC/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘PAC’
    finding HTML links ... done
    BSPLeaveCenter                          html  
    JaccardSM                               html  
    MAN                                     html  
    MINetworkPlot_topEdges                  html  
    MINetwork_matrix_topEdges               html  
    MINetwork_simplified_topEdges           html  
    PAC                                     html  
    aggregateData                           html  
    annotateClades                          html  
    annotationMatrix_withSubpopProp         html  
    constellationPlot                       html  
    fmeasure                                html  
    getAverageSpreadOf2SubpopClades         html  
    getExtraneousCladeSubpopulations        html  
    getRepresentativeNetworks               html  
    heatmapInput                            html  
    outputNetworks_topEdges_matrix          html  
    outputRepresentativeNetworks_topEdges   html  
    recordWithinClusterSpread               html  
    refineSubpopulationLabels               html  
    renamePrunedSubpopulations              html  
    runElbowPointAnalysis                   html  
    samplePass                              html  
** 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 (PAC)