* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘missSOM’ ...
** package ‘missSOM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/RtmpledwkV/R.INSTALL239da656a3c1d7/missSOM/src'
g++-13 -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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-13 -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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c distance-functions.cpp -o distance-functions.o
g++-13 -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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c imputeSOM.cpp -o imputeSOM.o
imputeSOM.cpp: In function ‘Rcpp::List RcppImputeSOM(Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::ExpressionVector, Rcpp::NumericMatrix, int, Rcpp::NumericVector, Rcpp::NumericVector, int, bool, Rcpp::IntegerVector, Rcpp::IntegerVector)’:
imputeSOM.cpp:177:45: warning: ‘threshold’ may be used uninitialized [-Wmaybe-uninitialized]
177 | tmp_bis = neighbourhoodFunctionPtr(pNeighbourhoodDistances[numCodes * nearest + cd], threshold);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
imputeSOM.cpp:63:25: note: ‘threshold’ was declared here
63 | double distance, tmp, threshold, alpha;
| ^~~~~~~~~
g++-13 -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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c map.cpp -o map.o
g++-13 -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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c neighbourhood-functions.cpp -o neighbourhood-functions.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o missSOM.so RcppExports.o distance-functions.o imputeSOM.o map.o neighbourhood-functions.o -fopenmp -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpledwkV/R.INSTALL239da656a3c1d7/missSOM/src'
make[1]: Entering directory '/tmp/RtmpledwkV/R.INSTALL239da656a3c1d7/missSOM/src'
make[1]: Leaving directory '/tmp/RtmpledwkV/R.INSTALL239da656a3c1d7/missSOM/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-missSOM/00new/missSOM/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘missSOM’
finding HTML links ... done
imputeSOM html
map.missSOM html
missSOM html
nir html
object.distances html
plot.missSOM html
summary.missSOM html
tricolor html
unit.distances html
wines html
yeast 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 (missSOM)