* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘missSOM’ ...
** this is package ‘missSOM’ version ‘1.0.1’
** package ‘missSOM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-10) 14.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpQ1OpER/R.INSTALL3e3f383db35d59/missSOM/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  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.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  -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-patched-gcc/Work/build/include/R.h:73,
                 from distance-functions.h:4,
                 from distance-functions.cpp:7:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/exceptions.h: In function ‘void Rcpp::Rf_warning(const char*, Args&& ...) [with Args = {const char*}]’:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include/R_ext/Error.h:85:17: warning: infinite recursion detected [-Winfinite-recursion]
   85 | #define warning Rf_warning
      |                 ^~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/exceptions.h:190:17: note: in expansion of macro ‘warning’
  190 |     inline void warning(const char* fmt, Args&&... args ) {
      |                 ^~~~~~~
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/RcppCommon.h:133,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp.h:27,
                 from distance-functions.h:5:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/exceptions.h:191:19: note: recursive call
  191 |         Rf_warning("%s", tfm::format(fmt, std::forward<Args>(args)... ).c_str());
      |         ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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  -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++-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  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c map.cpp -o map.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  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c neighbourhood-functions.cpp -o neighbourhood-functions.o
g++-14 -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 '/home/hornik/tmp/scratch/RtmpQ1OpER/R.INSTALL3e3f383db35d59/missSOM/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpQ1OpER/R.INSTALL3e3f383db35d59/missSOM/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpQ1OpER/R.INSTALL3e3f383db35d59/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)