Install log for 'covdepGE'

* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘covdepGE’ ...
** package ‘covdepGE’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
using C++11
make[1]: Entering directory '/tmp/RtmpB2xrJQ/R.INSTALL331cd426d27730/covdepGE/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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c code.cpp -o code.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c covdepGE_c.cpp -o covdepGE_c.o
covdepGE_c.cpp: In function ‘Rcpp::List grid_search_c(const arma::colvec&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::colvec&, const arma::colvec&, const arma::colvec&, double, int)’:
covdepGE_c.cpp:346:5: warning: ‘elbo_best’ may be used uninitialized [-Wmaybe-uninitialized]
  346 |     if (elbo_best <  elbo_new or j == 0){
      |     ^~
covdepGE_c.cpp:319:10: note: ‘elbo_best’ was declared here
  319 |   double elbo_best, elbo_new;
      |          ^~~~~~~~~
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:25,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
                 from covdepGE_c.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:465:46,
    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:489:40,
    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:532:13,
    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:525:46,
    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:514:34,
    inlined from ‘static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create__dispatch(Rcpp::traits::true_type, const T1&, const T2&, const T3&, const T4&, const T5&, const T6&, const T7&, const T8&, const T9&) [with T1 = Rcpp::traits::named_object<double>; T2 = Rcpp::traits::named_object<arma::Mat<double> >; T3 = Rcpp::traits::named_object<arma::Mat<double> >; T4 = Rcpp::traits::named_object<arma::Mat<double> >; T5 = Rcpp::traits::named_object<double>; T6 = Rcpp::traits::named_object<double>; T7 = Rcpp::traits::named_object<double>; T8 = Rcpp::traits::named_object<arma::Col<double> >; T9 = 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/generated/Vector__create.h:484:24,
    inlined from ‘static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&, const T3&, const T4&, const T5&, const T6&, const T7&, const T8&, const T9&) [with T1 = Rcpp::traits::named_object<double>; T2 = Rcpp::traits::named_object<arma::Mat<double> >; T3 = Rcpp::traits::named_object<arma::Mat<double> >; T4 = Rcpp::traits::named_object<arma::Mat<double> >; T5 = Rcpp::traits::named_object<double>; T6 = Rcpp::traits::named_object<double>; T7 = Rcpp::traits::named_object<double>; T8 = Rcpp::traits::named_object<arma::Col<double> >; T9 = 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/generated/Vector__create.h:447:49,
    inlined from ‘Rcpp::List grid_search_c(const arma::colvec&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::colvec&, const arma::colvec&, const arma::colvec&, double, int)’ at covdepGE_c.cpp:363:40:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/internal/wrap.h:442:41: warning: ‘ssq_best’ may be used uninitialized [-Wmaybe-uninitialized]
  442 |             r_vector_start<RTYPE>(x)[0] = object;
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
covdepGE_c.cpp: In function ‘Rcpp::List grid_search_c(const arma::colvec&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::colvec&, const arma::colvec&, const arma::colvec&, double, int)’:
covdepGE_c.cpp:325:10: note: ‘ssq_best’ was declared here
  325 |   double ssq_best, sbsq_best, pip_best;
      |          ^~~~~~~~
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:465:46,
    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:489:40,
    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:532:13,
    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:525:46,
    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:514:34,
    inlined from ‘static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create__dispatch(Rcpp::traits::true_type, const T1&, const T2&, const T3&, const T4&, const T5&, const T6&, const T7&, const T8&, const T9&) [with T1 = Rcpp::traits::named_object<double>; T2 = Rcpp::traits::named_object<arma::Mat<double> >; T3 = Rcpp::traits::named_object<arma::Mat<double> >; T4 = Rcpp::traits::named_object<arma::Mat<double> >; T5 = Rcpp::traits::named_object<double>; T6 = Rcpp::traits::named_object<double>; T7 = Rcpp::traits::named_object<double>; T8 = Rcpp::traits::named_object<arma::Col<double> >; T9 = 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/generated/Vector__create.h:485:24,
    inlined from ‘static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&, const T3&, const T4&, const T5&, const T6&, const T7&, const T8&, const T9&) [with T1 = Rcpp::traits::named_object<double>; T2 = Rcpp::traits::named_object<arma::Mat<double> >; T3 = Rcpp::traits::named_object<arma::Mat<double> >; T4 = Rcpp::traits::named_object<arma::Mat<double> >; T5 = Rcpp::traits::named_object<double>; T6 = Rcpp::traits::named_object<double>; T7 = Rcpp::traits::named_object<double>; T8 = Rcpp::traits::named_object<arma::Col<double> >; T9 = 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/generated/Vector__create.h:447:49,
    inlined from ‘Rcpp::List grid_search_c(const arma::colvec&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::colvec&, const arma::colvec&, const arma::colvec&, double, int)’ at covdepGE_c.cpp:363:40:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/internal/wrap.h:442:41: warning: ‘sbsq_best’ may be used uninitialized [-Wmaybe-uninitialized]
  442 |             r_vector_start<RTYPE>(x)[0] = object;
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
covdepGE_c.cpp: In function ‘Rcpp::List grid_search_c(const arma::colvec&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::colvec&, const arma::colvec&, const arma::colvec&, double, int)’:
covdepGE_c.cpp:325:20: note: ‘sbsq_best’ was declared here
  325 |   double ssq_best, sbsq_best, pip_best;
      |                    ^~~~~~~~~
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:465:46,
    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:489:40,
    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:532:13,
    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:525:46,
    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:514:34,
    inlined from ‘static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create__dispatch(Rcpp::traits::true_type, const T1&, const T2&, const T3&, const T4&, const T5&, const T6&, const T7&, const T8&, const T9&) [with T1 = Rcpp::traits::named_object<double>; T2 = Rcpp::traits::named_object<arma::Mat<double> >; T3 = Rcpp::traits::named_object<arma::Mat<double> >; T4 = Rcpp::traits::named_object<arma::Mat<double> >; T5 = Rcpp::traits::named_object<double>; T6 = Rcpp::traits::named_object<double>; T7 = Rcpp::traits::named_object<double>; T8 = Rcpp::traits::named_object<arma::Col<double> >; T9 = 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/generated/Vector__create.h:486:24,
    inlined from ‘static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&, const T3&, const T4&, const T5&, const T6&, const T7&, const T8&, const T9&) [with T1 = Rcpp::traits::named_object<double>; T2 = Rcpp::traits::named_object<arma::Mat<double> >; T3 = Rcpp::traits::named_object<arma::Mat<double> >; T4 = Rcpp::traits::named_object<arma::Mat<double> >; T5 = Rcpp::traits::named_object<double>; T6 = Rcpp::traits::named_object<double>; T7 = Rcpp::traits::named_object<double>; T8 = Rcpp::traits::named_object<arma::Col<double> >; T9 = 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/generated/Vector__create.h:447:49,
    inlined from ‘Rcpp::List grid_search_c(const arma::colvec&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::colvec&, const arma::colvec&, const arma::colvec&, double, int)’ at covdepGE_c.cpp:363:40:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/internal/wrap.h:442:41: warning: ‘pip_best’ may be used uninitialized [-Wmaybe-uninitialized]
  442 |             r_vector_start<RTYPE>(x)[0] = object;
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
covdepGE_c.cpp: In function ‘Rcpp::List grid_search_c(const arma::colvec&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::colvec&, const arma::colvec&, const arma::colvec&, double, int)’:
covdepGE_c.cpp:325:31: note: ‘pip_best’ was declared here
  325 |   double ssq_best, sbsq_best, pip_best;
      |                               ^~~~~~~~
g++-13 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o covdepGE.so RcppExports.o code.o covdepGE_c.o -fopenmp -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/RtmpB2xrJQ/R.INSTALL331cd426d27730/covdepGE/src'
make[1]: Entering directory '/tmp/RtmpB2xrJQ/R.INSTALL331cd426d27730/covdepGE/src'
make[1]: Leaving directory '/tmp/RtmpB2xrJQ/R.INSTALL331cd426d27730/covdepGE/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-covdepGE/00new/covdepGE/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘covdepGE’
    finding HTML links ... done
    covdepGE-package                        html  
    covdepGE                                html  
    generateData                            html  
    inclusionCurve                          html  
    matViz                                  html  
    plot.covdepGE                           html  
*** copying figures
** 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 (covdepGE)