* installing *source* package 'ProFAST' ...
** this is package 'ProFAST' version '1.6'
** package 'ProFAST' 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_02_09_03_13_2588/Rtmp6fbolq/R.INSTALL1a2f4bb3757a/ProFAST/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" "-DARMA_64BIT_WORD=1" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DR_removebatch.cpp -o DR_removebatch.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from DR_removebatch.cpp:5:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" "-DARMA_64BIT_WORD=1" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from RcppExports.cpp:4:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" "-DARMA_64BIT_WORD=1" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c alignExp.cpp -o alignExp.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from alignExp.cpp:3:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
alignExp.cpp: In function 'Rcpp::List correct_one_gene(const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const arma::mat&, const Rcpp::List&, const arma::vec&, const arma::vec&, const arma::vec&, const arma::vec&, const arma::vec&, const int&, const double&, const bool&)':
alignExp.cpp:165:8: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
165 | if(M != Tm.n_rows){
| ~~^~~~~~~~~~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" "-DARMA_64BIT_WORD=1" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c alignExps.cpp -o alignExps.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from alignExps.cpp:3:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
alignExps.cpp: In function 'Rcpp::List correct_genes(const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const arma::mat&, const Rcpp::List&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const int&, const double&, const bool&)':
alignExps.cpp:254:8: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
254 | if(M != Tm.n_rows){
| ~~^~~~~~~~~~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" "-DARMA_64BIT_WORD=1" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cofast_util.cpp -o cofast_util.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from cofast_util.cpp:2:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" "-DARMA_64BIT_WORD=1" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c profast.cpp -o profast.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from profast.cpp:5:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
profast.cpp: In function 'Rcpp::List profast_g_cpp(const Rcpp::List&, const Rcpp::List&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::cube&, const Rcpp::List&, const int&, const double&, const bool&, const bool&, const bool&)':
profast.cpp:406:7: warning: variable 'n' set but not used [-Wunused-but-set-variable]
406 | int n;
| ^
g++ -std=gnu++17 -shared -s -static-libgcc -o ProFAST.dll tmp.def DR_removebatch.o RcppExports.o alignExp.o alignExps.o cofast_util.o profast.o -LD:/RCompile/recent/R-4.5.1/bin/x64 -lRlapack -LD:/RCompile/recent/R-4.5.1/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-4.5.1/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2025_09_02_09_03_13_2588/Rtmp6fbolq/R.INSTALL1a2f4bb3757a/ProFAST/src'
make[1]: Entering directory '/d/temp/2025_09_02_09_03_13_2588/Rtmp6fbolq/R.INSTALL1a2f4bb3757a/ProFAST/src'
make[1]: Leaving directory '/d/temp/2025_09_02_09_03_13_2588/Rtmp6fbolq/R.INSTALL1a2f4bb3757a/ProFAST/src'
installing to d:/Rcompile/CRANpkg/lib/4.5/00LOCK-ProFAST/00new/ProFAST/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 'ProFAST' as ProFAST_1.6.zip
* DONE (ProFAST)