Install log for 'coreCollection'

* installing *source* package ‘coreCollection’ ...
** package ‘coreCollection’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/coreCollection/src'
g++-13 -std=gnu++17 -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 CoreAlgorithm.cpp -o CoreAlgorithm.o
g++-13 -std=gnu++17 -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 CoreAlgorithmRandomDescent.cpp -o CoreAlgorithmRandomDescent.o
CoreAlgorithmRandomDescent.cpp: In member function 'virtual Rcpp::IntegerVector CoreAlgorithmRandomDescent::getCore(CoreMethod&)':
CoreAlgorithmRandomDescent.cpp:10:7: warning: unused variable 'steps' [-Wunused-variable]
   10 |   int steps=0;
      |       ^~~~~
g++-13 -std=gnu++17 -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 CoreCollection.cpp -o CoreCollection.o
CoreCollection.cpp: In function 'Rcpp::IntegerVector computeCore(std::string, std::string, Rcpp::NumericMatrix&, Rcpp::List&)':
CoreCollection.cpp:147:3: warning: deleting object of polymorphic class type 'CoreMethod' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
  147 |   delete m;
      |   ^~~~~~~~
CoreCollection.cpp:148:3: warning: deleting object of polymorphic class type 'CoreAlgorithm' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
  148 |   delete a;
      |   ^~~~~~~~
g++-13 -std=gnu++17 -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 CoreMethod.cpp -o CoreMethod.o
g++-13 -std=gnu++17 -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 CoreMethodAccessionNearestEntry.cpp -o CoreMethodAccessionNearestEntry.o
g++-13 -std=gnu++17 -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 CoreMethodEntryEntry.cpp -o CoreMethodEntryEntry.o
CoreMethodEntryEntry.cpp: In member function 'virtual Rcpp::IntegerVector CoreMethodEntryEntry::adjustRandomNeighbour(Rcpp::IntegerVector, int)':
CoreMethodEntryEntry.cpp:7:76: warning: unused variable 'l' [-Wunused-variable]
    7 |   int nl, n = selectedRandomPositions.length(), N = distanceMatrix.nrow(), l=c.length();
      |                                                                            ^
CoreMethodEntryEntry.cpp: In static member function 'static double CoreMethodEntryEntry::measure(Rcpp::NumericMatrix&, Rcpp::IntegerVector&)':
CoreMethodEntryEntry.cpp:73:10: warning: unused variable 'd' [-Wunused-variable]
   73 |   double d, nd, sumOfDistances = 0.0;
      |          ^
CoreMethodEntryEntry.cpp:73:13: warning: unused variable 'nd' [-Wunused-variable]
   73 |   double d, nd, sumOfDistances = 0.0;
      |             ^~
g++-13 -std=gnu++17 -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 CoreMethodEntryNearestEntry.cpp -o CoreMethodEntryNearestEntry.o
g++-13 -std=gnu++17 -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 CoreSelection.cpp -o CoreSelection.o
CoreMethodEntryNearestEntry.cpp: In member function 'virtual Rcpp::IntegerVector CoreMethodEntryNearestEntry::adjustRandomNeighbour(Rcpp::IntegerVector, int)':
CoreMethodEntryNearestEntry.cpp:7:76: warning: unused variable 'l' [-Wunused-variable]
    7 |   int nl, n = selectedRandomPositions.length(), N = distanceMatrix.nrow(), l=c.length();
      |                                                                            ^
g++-13 -std=gnu++17 -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
CoreSelection.cpp: In static member function 'static Rcpp::IntegerVector CoreSelection::computeRandomSelection(Rcpp::NumericMatrix&, int, Rcpp::IntegerVector&)':
CoreSelection.cpp:141:7: warning: unused variable 'N' [-Wunused-variable]
  141 |   int N = dist.nrow();
      |       ^
g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o coreCollection.so CoreAlgorithm.o CoreAlgorithmRandomDescent.o CoreCollection.o CoreMethod.o CoreMethodAccessionNearestEntry.o CoreMethodEntryEntry.o CoreMethodEntryNearestEntry.o CoreSelection.o RcppExports.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/coreCollection/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/coreCollection/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/coreCollection/src'
installing to /data/gannet/ripley/R/packages/tests-devel/coreCollection.Rcheck/00LOCK-coreCollection/00new/coreCollection/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 (coreCollection)