* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘bayou’ ...
** this is package ‘bayou’ version ‘2.3.2’
** package ‘bayou’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-12) 14.3.0’
using C++17
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpWTpG3W/R.INSTALL1939c4364f878a/bayou/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'/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++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'/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 branches.cpp -o branches.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'/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 threepoint.cpp -o threepoint.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/RcppCommon.h:188,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:26,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:32,
                 from threepoint.cpp:1:
In function ‘SEXPREC* Rcpp::internal::primitive_wrap__impl__cast(const T&, Rcpp::traits::false_type) [with T = double]’,
    inlined from ‘SEXPREC* Rcpp::internal::primitive_wrap__impl(const T&, Rcpp::traits::r_type_primitive_tag) [with T = double]’ at /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/internal/wrap.h:471:46,
    inlined from ‘SEXPREC* Rcpp::internal::primitive_wrap(const T&) [with T = double]’ at /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/internal/wrap.h:495:40,
    inlined from ‘SEXPREC* Rcpp::internal::wrap_dispatch(const T&, Rcpp::traits::wrap_type_primitive_tag) [with T = double]’ at /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/internal/wrap.h:744:34,
    inlined from ‘SEXPREC* Rcpp::wrap(const T&) [with T = double]’ at /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/internal/wrap_end.h:30:38,
    inlined from ‘static SEXPREC* Rcpp::internal::generic_element_converter<RTYPE>::get(const T&) [with T = double; int RTYPE = 19]’ at /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/converter.h:80:23,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element__dispatch__isArgument(Rcpp::traits::false_type, iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<double>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:530:13,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element__dispatch(Rcpp::traits::true_type, iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<double>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:523:46,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element(iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<double>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:512:34,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<double>; TArgs = {Rcpp::traits::named_object<arma::Col<double> >}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:1169:24,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<arma::Col<double> >; TArgs = {Rcpp::traits::named_object<double>, Rcpp::traits::named_object<arma::Col<double> >}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
    inlined from ‘static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create__dispatch(Rcpp::traits::true_type, const T& ...) [with T = {Rcpp::traits::named_object<arma::Col<double> >, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<arma::Col<double> >}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:1146:29,
    inlined from ‘static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T& ...) [with T = {Rcpp::traits::named_object<arma::Col<double> >, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<arma::Col<double> >}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:1128:50,
    inlined from ‘SEXPREC* C_transf_branch_lengths(SEXP, int, Rcpp::NumericVector, double)’ at threepoint.cpp:148:30:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/internal/wrap.h:448:41: warning: ‘root’ may be used uninitialized [-Wmaybe-uninitialized]
  448 |             r_vector_start<RTYPE>(x)[0] = object;
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
threepoint.cpp: In function ‘SEXPREC* C_transf_branch_lengths(SEXP, int, Rcpp::NumericVector, double)’:
threepoint.cpp:102:20: note: ‘root’ was declared here
  102 |     double d1, d2, root;
      |                    ^~~~
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'/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 weightmatrix.cpp -o weightmatrix.o
weightmatrix.cpp: In function ‘SEXPREC* C_weightmatrix(SEXP, SEXP)’:
weightmatrix.cpp:81:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   81 |         for(int j=0; j < mstart.n_rows; ++j){
      |                      ~~^~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o bayou.so RcppExports.o branches.o threepoint.o weightmatrix.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpWTpG3W/R.INSTALL1939c4364f878a/bayou/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpWTpG3W/R.INSTALL1939c4364f878a/bayou/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpWTpG3W/R.INSTALL1939c4364f878a/bayou/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-bayou/00new/bayou/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘bayou’
    finding HTML links ... done
    Lposterior                              html  
    OU.lik                                  html  
    OU.repar                                html  
    OUphenogram                             html  
    OUwie2bayou                             html  
    QG.alpha                                html  
    QG.sig2                                 html  
    bayou-deprecated                        html  
    bayou-package                           html  
    bayou.checkModel                        html  
    bayou.lik                               html  
    bayou.makeMCMC                          html  
    bayou2OUwie                             html  
    cdpois                                  html  
    combine.chains                          html  
    dataSim                                 html  
    dhalfcauchy                             html  
    dloc                                    html  
    dsb                                     html  
    gelman.R                                html  
    identifyBranches                        html  
    load.bayou                              html  
    make.powerposteriorFn                   html  
    make.prior                              html  
    make.refFn                              html  
    makeBayouModel                          html  
    makeTransparent                         html  
    model.OU                                html  
    parmap.W                                html  
    pars2simmap                             html  
    phenogram.density                       html  
    plot.bayouMCMC                          html  
    plot.ssMCMC                             html  
    plotBayoupars                           html  
    plotBranchHeatMap                       html  
    plotOUtreesim                           html  
    plotRegimes                             html  
    plotShiftSummaries                      html  
    plotSimmap.mcmc                         html  
    print.bayouFit                          html  
    print.bayouMCMC                         html  
    print.priorFn                           html  
    print.refFn                             html  
    print.ssMCMC                            html  
    priorSim                                html  
    pull.pars                               html  
    regime.plot                             html  
    set.burnin                              html  
    shiftSummaries                          html  
    simmapW                                 html  
    summary.bayouMCMC                       html  
** 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 (bayou)