Install log for 'hdflex'

* installing *source* package ‘hdflex’ ...
** package ‘hdflex’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (GCC) 13.2.0’
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/hdflex/src'
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c dsc.cpp -o dsc.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c init.c -o init.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c stsc.cpp -o stsc.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c tvc.cpp -o tvc.o
stsc.cpp: In function 'Rcpp::List init_tvc_(const arma::vec&, const arma::mat&, const int&, const int&, const arma::vec&, const arma::vec&)':
stsc.cpp:26:43: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
   26 |                for (unsigned int j = 0; j < n_signal; j++) {
      |                                         ~~^~~~~~~~~~
stsc.cpp:60:24: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'const int' [-Wsign-compare]
   60 |                   if(j < n_sim_sig) {
      |                      ~~^~~~~~~~~~~
stsc.cpp: In function 'Rcpp::List dsc_init_(const int&, const int&, const int&, Rcpp::IntegerVector)':
stsc.cpp:285:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'const int' [-Wsign-compare]
  285 |       for (unsigned int g=0; g<n_gamma; g++) {
      |                              ~^~~~~~~~
stsc.cpp: In function 'void dsc_dpll_cands_(Rcpp::NumericVector, const double&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const double&, const int&, Rcpp::Nullable<const Rcpp::Vector<14, Rcpp::PreserveStorage>&>, Rcpp::Nullable<const Rcpp::Vector<14, Rcpp::PreserveStorage>&>, Rcpp::Nullable<const Rcpp::Vector<14, Rcpp::PreserveStorage>&>)':
stsc.cpp:400:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  400 |       for (unsigned int i=0; i<n_cands; i++) {
      |                              ~^~~~~~~~
stsc.cpp: In function 'void dsc_dpll_comb_(Rcpp::NumericVector&, const double&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const double&, const int&, Rcpp::Nullable<const Rcpp::Vector<14, Rcpp::PreserveStorage>&>, Rcpp::Nullable<const Rcpp::Vector<14, Rcpp::PreserveStorage>&>, Rcpp::Nullable<const Rcpp::Vector<14, Rcpp::PreserveStorage>&>)':
stsc.cpp:504:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  504 |       for (unsigned int i=0; i<n_combs; i++) {
      |                              ~^~~~~~~~
stsc.cpp: In function 'Rcpp::List stsc_loop(const arma::vec&, Rcpp::Nullable<const Rcpp::Matrix<14>&>, Rcpp::Nullable<const Rcpp::Matrix<14>&>, const int&, const arma::vec&, const arma::vec&, const int&, const Rcpp::NumericVector&, const Rcpp::IntegerVector&, const double&, const int&, const int&, const bool&, Rcpp::Nullable<const Rcpp::Vector<14, Rcpp::PreserveStorage>&>, Rcpp::Nullable<const Rcpp::Vector<14, Rcpp::PreserveStorage>&>, Rcpp::Nullable<const Rcpp::Vector<14, Rcpp::PreserveStorage>&>)':
stsc.cpp:767:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  767 |       for (unsigned int t=0; t<(tlength-1); t++ ) {
      |                              ~^~~~~~~~~~~~
stsc.cpp:802:16: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  802 |          if (t == (burn_in_tvc-1)) {
      |              ~~^~~~~~~~~~~~~~~~~~
stsc.cpp:812:16: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  812 |          if (t == (burn_in_dsc-1)) {
      |              ~~^~~~~~~~~~~~~~~~~~
tvc.cpp: In function 'Rcpp::List init_tvc_forecast(arma::vec&, arma::vec&, int)':
tvc.cpp:62:30: warning: variable 'var_x' set but not used [-Wunused-but-set-variable]
   62 |     double intercept, var_y, var_x, h;
      |                              ^~~~~
g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o hdflex.so RcppExports.o dsc.o init.o stsc.o tvc.o -fopenmp -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/hdflex/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/hdflex/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/hdflex/src'
installing to /data/gannet/ripley/R/packages/tests-devel/hdflex.Rcheck/00LOCK-hdflex/00new/hdflex/libs
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** 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 (hdflex)