* 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++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpQ9h7pL/R.INSTALL3c0851156da149/qtlpoly/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'/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
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++-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'/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++-14 -std=gnu++17 -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 '/home/hornik/tmp/scratch/RtmpQ9h7pL/R.INSTALL3c0851156da149/qtlpoly/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpQ9h7pL/R.INSTALL3c0851156da149/qtlpoly/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpQ9h7pL/R.INSTALL3c0851156da149/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
fit_model2 html
hexafake html
maps4x html
maps6x html
mmer_adapted html
modify_qtl html
null_model html
null_model2 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
read_data2 html
remim html
remim2 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)