* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘TransPhylo’ ...
** this is package ‘TransPhylo’ version ‘1.4.5’
** package ‘TransPhylo’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-10) 14.3.0’
using C++11
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmphf1v8C/R.INSTALL1a014d7dc5c848/TransPhylo/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 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 probPTreeGivenTTree.cpp -o probPTreeGivenTTree.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 probTTree.cpp -o probTTree.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o TransPhylo.so RcppExports.o probPTreeGivenTTree.o probTTree.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmphf1v8C/R.INSTALL1a014d7dc5c848/TransPhylo/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmphf1v8C/R.INSTALL1a014d7dc5c848/TransPhylo/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmphf1v8C/R.INSTALL1a014d7dc5c848/TransPhylo/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-TransPhylo/00new/TransPhylo/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘TransPhylo’
    finding HTML links ... done
    TransPhylo-package                      html  
    as.mcmc.resTransPhylo                   html  
    computeMatTDist                         html  
    computeMatWIW                           html  
    consTTree                               html  
    convertToCoda                           html  
    dateLastSample                          html  
    extractCTree                            html  
    extractPTree                            html  
    extractTTree                            html  
    getGenerationTimeDist                   html  
    getIncidentCases                        html  
    getInfectionTimeDist                    html  
    getOffspringDist                        html  
    getSamplingTimeDist                     html  
    inferTTree                              html  
    infer_multittree_share_param            html  
    makeCTreeFromPTree                      html  
    makeTTree                               html  
    medTTree                                html  
    phyloFromPTree                          html  
    plot.ctree                              html  
    plot.ptree                              html  
    plot.resTransPhylo                      html  
    plot.ttree                              html  
    plotCTree                               html  
    plotTTree                               html  
    plotTTree2                              html  
    plotTraces                              html  
    print.ctree                             html  
    print.ptree                             html  
    print.resTransPhylo                     html  
    print.ttree                             html  
    probPTreeGivenTTree                     html  
    probPTreeGivenTTreeR                    html  
    probTTree                               html  
    probTTreeR                              html  
    ptreeFromPhylo                          html  
    selectTTree                             html  
    simulateOutbreak                        html  
    summary.resTransPhylo                   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 (TransPhylo)