* installing *source* package 'ProFAST' ...
** package 'ProFAST' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++.exe (GCC) 12.3.0'
make[1]: Entering directory '/d/temp/RtmpILcPnm/R.INSTALL1ade84c8e6073/ProFAST/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/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/4.3/Rcpp/include/Rcpp/platform/compiler.h:100,
from D:/RCompile/CRANpkg/lib/4.3/Rcpp/include/Rcpp/r/headers.h:62,
from D:/RCompile/CRANpkg/lib/4.3/Rcpp/include/RcppCommon.h:30,
from D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from D:/RCompile/CRANpkg/lib/4.3/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::Mat<double> >&, arma::field<arma::Col<long long int> >&, arma::field<arma::Mat<double> >&, const arma::mat&, const arma::mat&, const arma::cube&, arma::cube&, const arma::field<arma::SpMat<double> >&, const arma::vec&, const arma::vec&, int, double&, arma::field<arma::Mat<double> >&, arma::field<arma::Mat<double> >&, arma::field<arma::Cube<double> >&, arma::field<arma::Cube<double> >&, arma::field<arma::Cube<double> >&, arma::field<arma::Cube<double> >&, arma::field<arma::Cube<double> >&, arma::field<arma::Cube<double> >&, 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-4.3.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/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-4.3.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/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/4.3/Rcpp/include/Rcpp/platform/compiler.h:100,
from D:/RCompile/CRANpkg/lib/4.3/Rcpp/include/Rcpp/r/headers.h:62,
from D:/RCompile/CRANpkg/lib/4.3/Rcpp/include/RcppCommon.h:30,
from D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from D:/RCompile/CRANpkg/lib/4.3/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-4.3.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/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/4.3/Rcpp/include/Rcpp/platform/compiler.h:100,
from D:/RCompile/CRANpkg/lib/4.3/Rcpp/include/Rcpp/r/headers.h:62,
from D:/RCompile/CRANpkg/lib/4.3/Rcpp/include/RcppCommon.h:30,
from D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from D:/RCompile/CRANpkg/lib/4.3/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-4.3.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I"d:/rtools43/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
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/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/4.3/Rcpp/include/Rcpp/platform/compiler.h:100,
from D:/RCompile/CRANpkg/lib/4.3/Rcpp/include/Rcpp/r/headers.h:62,
from D:/RCompile/CRANpkg/lib/4.3/Rcpp/include/RcppCommon.h:30,
from D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from D:/RCompile/CRANpkg/lib/4.3/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 cofast_util.o profast.o -LD:/RCompile/recent/R-4.3.3/bin/x64 -lRlapack -LD:/RCompile/recent/R-4.3.3/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-4.3.3/bin/x64 -lR
make[1]: Leaving directory '/d/temp/RtmpILcPnm/R.INSTALL1ade84c8e6073/ProFAST/src'
make[1]: Entering directory '/d/temp/RtmpILcPnm/R.INSTALL1ade84c8e6073/ProFAST/src'
make[1]: Leaving directory '/d/temp/RtmpILcPnm/R.INSTALL1ade84c8e6073/ProFAST/src'
installing to d:/Rcompile/CRANpkg/lib/4.3/00LOCK-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_1.4.zip
* DONE (ProFAST)