* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘qtlpoly’ ...
** package ‘qtlpoly’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
using C++11
make[1]: Entering directory '/tmp/RtmpdJwS1V/R.INSTALL3d9ce8326d877e/qtlpoly/src'
g++-13 -std=gnu++11 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c MNR.cpp -o MNR.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:26,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
                 from MNR.cpp:6:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: ‘#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed’
  321 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |                                                                                      ^
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: ‘#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead’
  326 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |                                                                           ^
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: ‘#pragma message: INFO: see the documentation for details’
  329 |   #pragma message ("INFO: see the documentation for details")
      |                                                             ^
MNR.cpp: In function ‘arma::vec varCols(const arma::mat&)’:
MNR.cpp:111:19: warning: ‘n’ may be used uninitialized [-Wmaybe-uninitialized]
  111 |     out(j) = M2/(n-1);
      |                 ~~^~~
MNR.cpp:101:9: note: ‘n’ was declared here
  101 |     int n;
      |         ^
MNR.cpp: In function ‘Rcpp::List MNR(const arma::mat&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const arma::vec&, int, double, double, const bool&, const bool&, const bool&, const bool&, const arma::vec&, const arma::vec&)’:
MNR.cpp:753:36: warning: ‘cycle2’ may be used uninitialized [-Wmaybe-uninitialized]
  753 |   arma::mat monitor2 = monitor.cols(0, cycle2);
      |                        ~~~~~~~~~~~~^~~~~~~~~~~
MNR.cpp:375:14: note: ‘cycle2’ was declared here
  375 |   int cycle, cycle2;
      |              ^~~~~~
MNR.cpp:744:20: warning: ‘llik’ may be used uninitialized [-Wmaybe-uninitialized]
  744 |   double AIC = (-2 * llik) + (2 * Xm.n_cols);
      |                ~~~~^~~~~~~
MNR.cpp:376:16: note: ‘llik’ was declared here
  376 |   double ldet, llik, llik0, delta_llik, checkP, seconds; // to store likelihoods and determinants
      |                ^~~~
g++-13 -std=gnu++11 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/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++11 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o qtlpoly.so MNR.o RcppExports.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpdJwS1V/R.INSTALL3d9ce8326d877e/qtlpoly/src'
make[1]: Entering directory '/tmp/RtmpdJwS1V/R.INSTALL3d9ce8326d877e/qtlpoly/src'
make[1]: Leaving directory '/tmp/RtmpdJwS1V/R.INSTALL3d9ce8326d877e/qtlpoly/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-qtlpoly/00new/qtlpoly/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘qtlpoly’
    finding HTML links ... done
    B2721                                   html  
    breeding_values                         html  
    feim                                    html  
    fit_model                               html  
    hexafake                                html  
    maps4x                                  html  
    maps6x                                  html  
    mmer_adapted                            html  
    modify_qtl                              html  
    null_model                              html  
    optimize_qtl                            html  
    permutations                            html  
    pheno4x                                 html  
    pheno6x                                 html  
    plot_profile                            html  
    plot_qtl                                html  
    plot_sint                               html  
    profile_qtl                             html  
    qtl_effects                             html  
    read_data                               html  
    remim                                   html  
    search_qtl                              html  
    simulate_qtl                            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 (qtlpoly)