Install log for 'pmartR'

* installing *source* package ‘pmartR’ ...
** this is package ‘pmartR’ version ‘2.5.0’
** package ‘pmartR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/pmartR/src'
g++ -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'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include    -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++ -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'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include    -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 calculate_cv.cpp -o calculate_cv.o
g++ -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'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include    -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 count_missing_cpp.cpp -o count_missing_cpp.o
g++ -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'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include    -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 imd_anova.cpp -o imd_anova.o
g++ -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'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include    -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 kw_rcpp.cpp -o kw_rcpp.o
imd_anova.cpp: In function ‘arma::mat fold_change_diff_na_okay(arma::mat, arma::mat)’:
imd_anova.cpp:154:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
  154 |         for(int k=0;k<of_int.size();k++){
      |                     ~^~~~~~~~~~~~~~
imd_anova.cpp: In function ‘Rcpp::List anova_cpp(arma::mat, Rcpp::NumericVector, int, arma::mat, arma::mat, arma::mat, arma::uvec, arma::uvec)’:
imd_anova.cpp:218:16: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const unsigned int’} and ‘int’ [-Wsign-compare]
  218 |   if (X.n_cols > m) {
      |       ~~~~~~~~~^~~
imd_anova.cpp:249:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
  249 |       for (int k = 0; k < continuous_covar_inds.size(); k++) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
imd_anova.cpp:259:31: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const unsigned int’} and ‘int’ [-Wsign-compare]
  259 |     if (group_ids_pred.n_elem > m) {
      |         ~~~~~~~~~~~~~~~~~~~~~~^~~
imd_anova.cpp: In function ‘Rcpp::List two_factor_anova_cpp(arma::mat, arma::mat, arma::mat, arma::colvec, arma::mat, arma::mat, arma::uvec, arma::uvec, int)’:
imd_anova.cpp:450:47: warning: ‘static out_eT arma::conv_to<out_eT>::from(const arma::Base<eT2, expr>&, const typename arma::arma_not_cx<in_eT>::result*) [with in_eT = double; T1 = arma::eOp<arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>, arma::eop_scalar_div_post>; out_eT = double; typename arma::arma_not_cx<in_eT>::result = double]’ is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
  450 |       sigma2_red = arma::conv_to<double>::from(residual_vec.t()*residual_vec/df_red);
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:496,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:32,
                 from imd_anova.cpp:1:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:72:1: note: declared here
   72 | conv_to<out_eT>::from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk)
      | ^~~~~~~~~~~~~~~
imd_anova.cpp:464:48: warning: ‘static out_eT arma::conv_to<out_eT>::from(const arma::Base<eT2, expr>&, const typename arma::arma_not_cx<in_eT>::result*) [with in_eT = double; T1 = arma::eOp<arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>, arma::eop_scalar_div_post>; out_eT = double; typename arma::arma_not_cx<in_eT>::result = double]’ is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
  464 |       sigma2_full = arma::conv_to<double>::from(residual_vec.t()*residual_vec/df_full);
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:72:1: note: declared here
   72 | conv_to<out_eT>::from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk)
      | ^~~~~~~~~~~~~~~
imd_anova.cpp:478:47: warning: ‘static out_eT arma::conv_to<out_eT>::from(const arma::Base<eT2, expr>&, const typename arma::arma_not_cx<in_eT>::result*) [with in_eT = double; T1 = arma::eOp<arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>, arma::eop_scalar_div_post>; out_eT = double; typename arma::arma_not_cx<in_eT>::result = double]’ is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
  478 |       sigma2_red = arma::conv_to<double>::from(residual_vec.t()*residual_vec/df_red);
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:72:1: note: declared here
   72 | conv_to<out_eT>::from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk)
      | ^~~~~~~~~~~~~~~
imd_anova.cpp:491:50: warning: ‘static out_eT arma::conv_to<out_eT>::from(const arma::Base<eT2, expr>&, const typename arma::arma_not_cx<in_eT>::result*) [with in_eT = double; T1 = arma::eOp<arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>, arma::eop_scalar_div_post>; out_eT = double; typename arma::arma_not_cx<in_eT>::result = double]’ is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
  491 |         sigma2_full = arma::conv_to<double>::from(residual_vec.t()*residual_vec/df_full);
      |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:72:1: note: declared here
   72 | conv_to<out_eT>::from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk)
      | ^~~~~~~~~~~~~~~
imd_anova.cpp:528:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
  528 |       for (int k = 0; k < continuous_covar_inds.size(); k++) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
imd_anova.cpp:541:31: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const unsigned int’} and ‘int’ [-Wsign-compare]
  541 |     if (group_ids_pred.n_elem > n_groups) {
      |         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
imd_anova.cpp: In function ‘Rcpp::List group_comparison_anova_cpp(arma::mat, arma::mat, arma::mat, arma::mat, arma::mat, arma::mat, arma::mat, arma::mat, arma::mat)’:
imd_anova.cpp:670:26: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = double; typename arma_scalar_only<T>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  670 |       if (arma::is_finite(t_tests(i,k)) && dof > 0) {
      |           ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:518:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
  167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
      | ^~~~~~~~~
g++ -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'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include    -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 nonmissing_per_grp.cpp -o nonmissing_per_grp.o
imd_anova.cpp: In function ‘Rcpp::List two_factor_anova_cpp(arma::mat, arma::mat, arma::mat, arma::colvec, arma::mat, arma::mat, arma::uvec, arma::uvec, int)’:
imd_anova.cpp:500:20: warning: ‘sigma2_full’ may be used uninitialized [-Wmaybe-uninitialized]
  500 |         sig_est(i) = sigma2_full;
      |         ~~~~~~~~~~~^~~~~~~~~~~~~
imd_anova.cpp:408:22: note: ‘sigma2_full’ was declared here
  408 |   double sigma2_red, sigma2_full;
      |                      ^~~~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o pmartR.so RcppExports.o calculate_cv.o count_missing_cpp.o imd_anova.o kw_rcpp.o nonmissing_per_grp.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/pmartR/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/pmartR/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/pmartR/src'
installing to /data/gannet/ripley/R/packages/tests-devel/pmartR.Rcheck/00LOCK-pmartR/00new/pmartR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (pmartR)