Install log for 'rtk'

* installing *source* package ‘rtk’ ...
** package ‘rtk’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (GCC) 13.2.0’
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
using C++11
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/rtk/src'
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c ClStr2Mat.cpp -o ClStr2Mat.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c IO.cpp -o IO.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c Math.cpp -o Math.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c Matrix.cpp -o Matrix.o
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);
      |             ^~~~~~~~~~~~~
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c RRare.cpp -o RRare.o
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++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c Rwrapper.cpp -o Rwrapper.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c register.c -o register.o
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++){
      |                      ~~^~~~~~~~~~~~~
g++-13 -std=gnu++11 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o rtk.so ClStr2Mat.o IO.o Math.o Matrix.o RRare.o RcppExports.o Rwrapper.o register.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/rtk/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/rtk/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/rtk/src'
installing to /data/gannet/ripley/R/packages/tests-devel/rtk.Rcheck/00LOCK-rtk/00new/rtk/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rtk)