* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘coreCollection’ ...
** package ‘coreCollection’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmptLhX4P/R.INSTALL14742133fd12b4/coreCollection/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CoreAlgorithm.cpp -o CoreAlgorithm.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CoreMethod.cpp -o CoreMethod.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CoreMethodAccessionNearestEntry.cpp -o CoreMethodAccessionNearestEntry.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CoreMethodEntryNearestEntry.cpp -o CoreMethodEntryNearestEntry.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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CoreSelection.cpp -o CoreSelection.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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o coreCollection.so CoreAlgorithm.o CoreAlgorithmRandomDescent.o CoreCollection.o CoreMethod.o CoreMethodAccessionNearestEntry.o CoreMethodEntryEntry.o CoreMethodEntryNearestEntry.o CoreSelection.o RcppExports.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmptLhX4P/R.INSTALL14742133fd12b4/coreCollection/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmptLhX4P/R.INSTALL14742133fd12b4/coreCollection/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmptLhX4P/R.INSTALL14742133fd12b4/coreCollection/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-coreCollection/00new/coreCollection/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘coreCollection’
finding HTML links ... done
CoreCollection html
finding level-2 HTML links ... done
computeAdjustedSelectionUsingRecomputeMethod
html
computeAdjustedSelectionUsingSplitMethod
html
computeCore html
computeRandomSelection html
coreCollection-package html
dot-CoreCollectionClass html
** 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)