* 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)