* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘coda.base’ ...
** package ‘coda.base’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/tmp/Rtmps8713Y/R.INSTALL4428660d88bc1/coda.base/src'
g++-13 -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++-13 -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 coda.cpp -o coda.o
g++-13 -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 principal_balances.cpp -o principal_balances.o
In file included from balance.h:5,
from principal_balances.cpp:5:
balance_evaluate.h: In constructor ‘MaximumVariance::MaximumVariance(std::map<int, arma::Col<unsigned int> >&, arma::mat&)’:
balance_evaluate.h:38:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<int, arma::Col<unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
38 | for(int i = 0; i < nodes0.size(); i++){
| ~~^~~~~~~~~~~~~~~
balance_evaluate.h:40:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<int, arma::Col<unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
40 | for(int j = 0; j < nodes0.size(); j++){
| ~~^~~~~~~~~~~~~~~
balance_evaluate.h: In member function ‘virtual double MaximumVariance::eval(arma::uvec&, arma::uvec&, int, int)’:
balance_evaluate.h:50:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
50 | for(unsigned int i=0; i<l;nL+=N[L[i++]]);
| ~^~
balance_evaluate.h:53:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
53 | for(unsigned int i=0; i<r;nR+=N[R[i++]]);
| ~^~
principal_balances.cpp: In function ‘void optimise_balance_using_pc(Balance<MaximumVariance>&, arma::mat&)’:
principal_balances.cpp:26:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
26 | for(int i = 0; i < Xsub.n_cols; i++){
| ~~^~~~~~~~~~~~~
principal_balances.cpp:28:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
28 | for(int j = 1; j < balance.nodes[i].n_elem; j++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~
principal_balances.cpp: In function ‘void optimise_using_pc_forcing_branch(Balance<MaximumVariance>&, arma::mat&, unsigned int)’:
principal_balances.cpp:112:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
112 | for(int i = 0; i < Xsub.n_cols; i++){
| ~~^~~~~~~~~~~~~
principal_balances.cpp:114:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
114 | for(int j = 1; j < balance.nodes[i].n_elem; j++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~
principal_balances.cpp: In function ‘arma::mat find_PB_using_pc_recursively_forcing_parents(arma::mat&)’:
principal_balances.cpp:383:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
383 | for(int i = 0; i < zeros.n_elem; i++) Xsub.col(i) = X.col(zeros[i]);
| ~~^~~~~~~~~~~~~~
balance.h: In instantiation of ‘void Balance<EB>::setWithLogContrastForceBranch(arma::vec, arma::uvec) [with EB = MaximumVariance; arma::vec = arma::Col<double>; arma::uvec = arma::Col<unsigned int>]’:
principal_balances.cpp:124:42: required from here
balance.h:111:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
111 | for(int i=1; i < forced.size(); i++){
| ~~^~~~~~~~~~~~~~~
In file included from balance.h:6:
balance_optimal.h: In instantiation of ‘void b(int, int, int, arma::uvec&, arma::uvec&, std::vector<arma::Col<unsigned int> >&, int*, EB&) [with EB = MaximumVariance; arma::uvec = arma::Col<unsigned int>]’:
balance_optimal.h:87:12: required from ‘void f(int, int, int, arma::uvec&, arma::uvec&, std::vector<arma::Col<unsigned int> >&, int*, EB&) [with EB = MaximumVariance; arma::uvec = arma::Col<unsigned int>]’
balance.h:80:10: required from ‘void Balance<EB>::setWithExhaustiveSearch() [with EB = MaximumVariance]’
principal_balances.cpp:13:34: required from here
balance_optimal.h:112:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
112 | while(A[nu] < mu - 1){
balance_optimal.h:132:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
132 | while(A[nu] < mu - 1){
principal_balances.cpp:410:49: warning: ‘bestR’ may be used uninitialized [-Wmaybe-uninitialized]
410 | bal(no_zeros).fill(-1.0/l * sqrt((double)l*bestR/(l+bestR)));
| ~~~~~~~~~^~~~~~
principal_balances.cpp:373:21: note: ‘bestR’ was declared here
373 | unsigned r = 0, bestR;
| ^~~~~
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o coda.base.so RcppExports.o coda.o principal_balances.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 '/tmp/Rtmps8713Y/R.INSTALL4428660d88bc1/coda.base/src'
make[1]: Entering directory '/tmp/Rtmps8713Y/R.INSTALL4428660d88bc1/coda.base/src'
make[1]: Leaving directory '/tmp/Rtmps8713Y/R.INSTALL4428660d88bc1/coda.base/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-coda.base/00new/coda.base/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 ‘coda.base’
finding HTML links ... done
alimentation html
alr_basis html
arctic_lake html
basis html
blood_mn html
bmi_activity html
cbalance_approx html
cc_basis html
cdp_basis html
cdp_partition html
center html
clr_basis html
coda.base html
composition html
coordinates html
dist html
eurostat_employment html
foraminiferals html
gmean html
house_expend html
household_budget html
ilr_basis html
mammals_milk html
milk_cows html
montana html
pairwise_basis html
parliament2017 html
pb_basis html
pc_basis html
petrafm html
plot_balance html
pollen html
pottery html
print.coda html
read_cdp html
sbp_basis html
serprot html
statistitian_time html
variation_array html
waste html
weibo_hotels 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 (coda.base)