* installing to library ‘/home/hornik/tmp/R.check/r-release-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 13.3.0-1) 13.3.0’
make[1]: Entering directory '/tmp/Rtmp34VNrN/R.INSTALL6a5c52ea4c6c/missSOM/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-release-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
In file included from /home/hornik/tmp/R.check/r-release-gcc/Work/build/include/R.h:73,
                 from distance-functions.h:4,
                 from distance-functions.cpp:7:
/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h: In function ‘void Rcpp::Rf_warning(const char*, Args&& ...) [with Args = {const char*}]’:
/home/hornik/tmp/R.check/r-release-gcc/Work/build/include/R_ext/Error.h:69:17: warning: infinite recursion detected [-Winfinite-recursion]
   69 | #define warning Rf_warning
      |                 ^~~~~~~~~~
/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h:46:13: note: in expansion of macro ‘warning’
   46 | inline void warning(const char* fmt, Args&&... args ) {
      |             ^~~~~~~
In file included from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include/Rcpp/exceptions.h:180,
                 from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include/RcppCommon.h:130,
                 from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include/Rcpp.h:27,
                 from distance-functions.h:5:
/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h:47:15: note: recursive call
   47 |     Rf_warning("%s", tfm::format(fmt, std::forward<Args>(args)... ).c_str());
      |     ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-release-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-release-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-release-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmp34VNrN/R.INSTALL6a5c52ea4c6c/missSOM/src'
make[1]: Entering directory '/tmp/Rtmp34VNrN/R.INSTALL6a5c52ea4c6c/missSOM/src'
make[1]: Leaving directory '/tmp/Rtmp34VNrN/R.INSTALL6a5c52ea4c6c/missSOM/src'
installing to /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-missSOM/00new/missSOM/libs
** R
** data
** 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 (missSOM)