* installing *source* package 'ProFAST' ... ** using staged installation ** libs using C++ compiler: 'g++.exe (GCC) 12.3.0' g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I"d:/rtools43/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 DR_removebatch.cpp:15: warning: "INT_MIN" redefined 15 | #define INT_MIN (-INT_MAX - 1) | In file included from d:\rtools43\x86_64-w64-mingw32.static.posix\include\stdlib.h:11, from d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\std_abs.h:38, from d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\cmath:47, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/platform/compiler.h:100, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/r/headers.h:62, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/RcppCommon.h:30, from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25, from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/RcppArmadillo.h:29, from DR_removebatch.cpp:5: d:\rtools43\x86_64-w64-mingw32.static.posix\include\limits.h:39: note: this is the location of the previous definition 39 | #define INT_MIN (-2147483647 - 1) | DR_removebatch.cpp: In function 'void runICM_sp_embed(const arma::field >&, arma::field >&, arma::field >&, const arma::mat&, const arma::mat&, const arma::cube&, arma::cube&, const arma::field >&, const arma::vec&, const arma::vec&, int, double&, arma::field >&, arma::field >&, arma::field >&, arma::field >&, arma::field >&, arma::field >&, arma::field >&, arma::field >&, const bool&)': DR_removebatch.cpp:432:7: warning: unused variable 'i' [-Wunused-variable] 432 | int i, iter, k, n; | ^ g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" "-DARMA_64BIT_WORD=1" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" "-DARMA_64BIT_WORD=1" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c alignExp.cpp -o alignExp.o alignExp.cpp:8: warning: "INT_MIN" redefined 8 | #define INT_MIN (-INT_MAX - 1) | In file included from d:\rtools43\x86_64-w64-mingw32.static.posix\include\stdlib.h:11, from d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\std_abs.h:38, from d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\cmath:47, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/platform/compiler.h:100, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/r/headers.h:62, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/RcppCommon.h:30, from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25, from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/RcppArmadillo.h:29, from alignExp.cpp:3: d:\rtools43\x86_64-w64-mingw32.static.posix\include\limits.h:39: note: this is the location of the previous definition 39 | #define INT_MIN (-2147483647 - 1) | 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){ | ~~^~~~~~~~~~~~ alignExp.cpp:180:7: warning: unused variable 'n' [-Wunused-variable] 180 | int n; | ^ g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" "-DARMA_64BIT_WORD=1" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c alignExps.cpp -o alignExps.o alignExps.cpp:8: warning: "INT_MIN" redefined 8 | #define INT_MIN (-INT_MAX - 1) | In file included from d:\rtools43\x86_64-w64-mingw32.static.posix\include\stdlib.h:11, from d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\std_abs.h:38, from d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\cmath:47, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/platform/compiler.h:100, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/r/headers.h:62, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/RcppCommon.h:30, from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25, from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/RcppArmadillo.h:29, from alignExps.cpp:3: d:\rtools43\x86_64-w64-mingw32.static.posix\include\limits.h:39: note: this is the location of the previous definition 39 | #define INT_MIN (-2147483647 - 1) | 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:255:8: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare] 255 | if(M != Tm.n_rows){ | ~~^~~~~~~~~~~~ g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" "-DARMA_64BIT_WORD=1" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c profast.cpp -o profast.o profast.cpp:14: warning: "INT_MIN" redefined 14 | #define INT_MIN (-INT_MAX - 1) | In file included from d:\rtools43\x86_64-w64-mingw32.static.posix\include\stdlib.h:11, from d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\std_abs.h:38, from d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\cmath:47, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/platform/compiler.h:100, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/r/headers.h:62, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/RcppCommon.h:30, from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25, from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/RcppArmadillo.h:29, from profast.cpp:5: d:\rtools43\x86_64-w64-mingw32.static.posix\include\limits.h:39: note: this is the location of the previous definition 39 | #define INT_MIN (-2147483647 - 1) | 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:408:7: warning: variable 'n' set but not used [-Wunused-but-set-variable] 408 | int n; | ^ g++ -std=gnu++17 -shared -s -static-libgcc -o ProFAST.dll tmp.def DR_removebatch.o RcppExports.o alignExp.o alignExps.o profast.o -LD:/RCompile/recent/R/bin/x64 -lRlapack -LD:/RCompile/recent/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR installing to d:/RCompile/CRANincoming/R-devel/lib/00LOCK-ProFAST/00new/ProFAST/libs/x64 ** R ** 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 * DONE (ProFAST)