* 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++.exe (GCC) 14.2.0'
make[1]: Entering directory '/d/temp/2025_09_25_01_50_00_17305/RtmpuGozkN/R.INSTALL15ec446272da2/pmartR/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/BH/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
In file included from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo:26,
from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo.h:32,
from RcppExports.cpp:4:
D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
373 | #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
| ^
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/BH/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calculate_cv.cpp -o calculate_cv.o
In file included from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo:26,
from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo.h:32,
from calculate_cv.cpp:50:
D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
373 | #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
| ^
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/BH/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c count_missing_cpp.cpp -o count_missing_cpp.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/BH/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imd_anova.cpp -o imd_anova.o
In file included from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo:26,
from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo.h:32,
from imd_anova.cpp:1:
D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
373 | #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
| ^
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 D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo:496:
D:/RCompile/CRANpkg/lib/4.6/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);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/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<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::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 D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo:518:
D:/RCompile/CRANpkg/lib/4.6/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)
| ^~~~~~~~~
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 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/BH/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kw_rcpp.cpp -o kw_rcpp.o
In file included from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo:26,
from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo.h:32,
from kw_rcpp.cpp:36:
D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
373 | #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
| ^
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/BH/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c nonmissing_per_grp.cpp -o nonmissing_per_grp.o
In file included from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo:26,
from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/RcppArmadillo.h:32,
from nonmissing_per_grp.cpp:1:
D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
373 | #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
| ^
g++ -std=gnu++17 -shared -s -static-libgcc -o pmartR.dll tmp.def RcppExports.o calculate_cv.o count_missing_cpp.o imd_anova.o kw_rcpp.o nonmissing_per_grp.o -LD:/RCompile/recent/R/bin/x64 -lRlapack -LD:/RCompile/recent/R/bin/x64 -lRblas -lgfortran -lquadmath -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2025_09_25_01_50_00_17305/RtmpuGozkN/R.INSTALL15ec446272da2/pmartR/src'
make[1]: Entering directory '/d/temp/2025_09_25_01_50_00_17305/RtmpuGozkN/R.INSTALL15ec446272da2/pmartR/src'
make[1]: Leaving directory '/d/temp/2025_09_25_01_50_00_17305/RtmpuGozkN/R.INSTALL15ec446272da2/pmartR/src'
installing to d:/Rcompile/CRANpkg/lib/4.6/00LOCK-pmartR/00new/pmartR/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'pmartR' as pmartR_2.5.0.zip
* DONE (pmartR)