* installing *source* package 'rtk' ...
** package 'rtk' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
using C++ compiler: 'g++.exe (GCC) 13.3.0'
using C++11
make[1]: Entering directory '/d/temp/2024_11_19_01_50_00_21579/Rtmpag1Q3h/R.INSTALL1a2487cef332c/rtk/src'
g++ -std=gnu++11 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClStr2Mat.cpp -o ClStr2Mat.o
In file included from Matrix.h:2,
from ClStr2Mat.h:2,
from ClStr2Mat.cpp:1:
IO.h:28: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
28 | #pragma warning(disable:4996)
|
g++ -std=gnu++11 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c IO.cpp -o IO.o
In file included from IO.cpp:1:
IO.h:28: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
28 | #pragma warning(disable:4996)
|
IO.cpp: In function 'void lineCntOut(options*)':
IO.cpp:74:19: warning: 'in' may be used uninitialized [-Wmaybe-uninitialized]
74 | while (getline((*in), line, '\n')) {
| ~~~~~~~^~~~~~~~~~~~~~~~~~~
IO.cpp:21:18: note: 'in' was declared here
21 | istream* in;
| ^~
g++ -std=gnu++11 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Math.cpp -o Math.o
g++ -std=gnu++11 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Matrix.cpp -o Matrix.o
In file included from Matrix.h:2,
from Matrix.cpp:1:
IO.h:28: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
28 | #pragma warning(disable:4996)
|
Matrix.cpp: In constructor 'Matrix::Matrix(std::string, std::string, std::vector<double>, std::vector<std::__cxx11::basic_string<char> >)':
Matrix.cpp:672:13: warning: unused variable 'ini_ColPerRow' [-Wunused-variable]
672 | int ini_ColPerRow = iniCols(in);
| ^~~~~~~~~~~~~
Matrix.cpp: In constructor 'Matrix::Matrix(std::string, std::string, std::vector<double>, std::vector<std::__cxx11::basic_string<char> >)':
Matrix.cpp:672:36: warning: 'in' may be used uninitialized [-Wmaybe-uninitialized]
672 | int ini_ColPerRow = iniCols(in);
| ~~~~~~~^~~~
Matrix.cpp:646:18: note: 'in' was declared here
646 | istream* in;
| ^~
Matrix.cpp: In constructor 'Matrix::Matrix(std::string, std::string, std::string, std::vector<std::__cxx11::basic_string<char> >&, bool, bool, bool)':
Matrix.cpp:797:36: warning: 'in' may be used uninitialized [-Wmaybe-uninitialized]
797 | int ini_ColPerRow = iniCols(in);
| ~~~~~~~^~~~
Matrix.cpp:771:18: note: 'in' was declared here
771 | istream* in;
| ^~
Matrix.cpp: In constructor 'Matrix::Matrix(std::string, std::string, bool)':
Matrix.cpp:980:36: warning: 'in' may be used uninitialized [-Wmaybe-uninitialized]
980 | int ini_ColPerRow = iniCols(in);
| ~~~~~~~^~~~
Matrix.cpp:958:18: note: 'in' was declared here
958 | istream* in;
| ^~
g++ -std=gnu++11 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RRare.cpp -o RRare.o
In file included from Matrix.h:2,
from ClStr2Mat.h:2,
from RRare.h:2,
from RRare.cpp:1:
IO.h:28: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
28 | #pragma warning(disable:4996)
|
RRare.cpp: In function 'int rarefyMain(options*, std::string, std::vector<std::vector<double> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<DivEsts*>&, std::vector<std::vector<std::vector<std::unordered_map<unsigned int, unsigned int> > > >&, std::vector<std::vector<std::__cxx11::basic_string<char> > >&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<std::__cxx11::basic_string<char> >&, bool)':
RRare.cpp:307:14: warning: unused variable 'writeFiles' [-Wunused-variable]
307 | bool writeFiles = false;
| ^~~~~~~~~~
g++ -std=gnu++11 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Rwrapper.cpp -o Rwrapper.o
In file included from Matrix.h:2,
from ClStr2Mat.h:2,
from RRare.h:2,
from Rwrapper.cpp:3:
IO.h:28: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
28 | #pragma warning(disable:4996)
|
Rwrapper.cpp: In function 'Rcpp::List returnRList(options*, std::vector<DivEsts*>&, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, bool, std::vector<std::vector<std::vector<std::unordered_map<unsigned int, unsigned int> > > >, unsigned int)':
Rwrapper.cpp:117:24: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
117 | for(int i=0; i < opts->write; i++){
| ~~^~~~~~~~~~~~~
gcc -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c register.c -o register.o
g++ -shared -s -static-libgcc -o rtk.dll tmp.def ClStr2Mat.o IO.o Math.o Matrix.o RRare.o RcppExports.o Rwrapper.o register.o -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.4.2/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2024_11_19_01_50_00_21579/Rtmpag1Q3h/R.INSTALL1a2487cef332c/rtk/src'
make[1]: Entering directory '/d/temp/2024_11_19_01_50_00_21579/Rtmpag1Q3h/R.INSTALL1a2487cef332c/rtk/src'
make[1]: Leaving directory '/d/temp/2024_11_19_01_50_00_21579/Rtmpag1Q3h/R.INSTALL1a2487cef332c/rtk/src'
installing to d:/Rcompile/CRANpkg/lib/4.4/00LOCK-rtk/00new/rtk/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 'rtk' as rtk_0.2.6.1.zip
* DONE (rtk)