* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘sommer’ ...
** package ‘sommer’ 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/RtmpPcNQq1/R.INSTALL29f14a6aeddcba/sommer/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'/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:5:
/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::mat dmat(const arma::mat&, const bool&, double)’:
MNR.cpp:306:7: warning: unused variable ‘p’ [-Wunused-variable]
306 | int p = X.n_cols;
| ^
MNR.cpp: In function ‘arma::rowvec scorecalc(const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, int, double)’:
MNR.cpp:453:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
453 | for (int i = 0; i < b.n_rows; ++i) {
| ~~^~~~~~~~~~
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::mat&, const bool&, int, double, double, const bool&, const bool&, const bool&, const bool&, const arma::vec&, const arma::vec&)’:
MNR.cpp:635:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
635 | for(int h=0; h < provX.n_cols ; h++){ // for each random effect unlist
| ~~^~~~~~~~~~~~~~
MNR.cpp: In function ‘Rcpp::List ai_mme_sp(const arma::sp_mat&, const Rcpp::List&, const arma::vec&, const Rcpp::List&, const arma::sp_mat&, const Rcpp::List&, const Rcpp::List&, const arma::sp_mat&, const bool&, int, double, double, double, const Rcpp::List&, const Rcpp::List&, const arma::mat&, const arma::vec&, const arma::vec&, const arma::vec&, const bool&)’:
MNR.cpp:1299:12: warning: unused variable ‘ok’ [-Wunused-variable]
1299 | bool ok = log_det(val, sign, arma::mat(Ai[i])); // calculate the logDet of the covariance matrix
| ^~
MNR.cpp:1522:14: warning: unused variable ‘ok’ [-Wunused-variable]
1522 | bool ok = log_det(val, sign, theta(i)); // form 2
| ^~
MNR.cpp:1570:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
1570 | for(int iRow = 0; iRow < partitionsP.n_rows; ++iRow){ // for each partition row
| ~~~~~^~~~~~~~~~~~~~~~~~~~
MNR.cpp:1588:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
1588 | for(int iRow = 0; iRow < lambdaProv.n_rows; ++iRow){
| ~~~~~^~~~~~~~~~~~~~~~~~~
MNR.cpp:1589:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
1589 | for(int iCol = 0; iCol < lambdaProv.n_cols; ++iCol){
| ~~~~~^~~~~~~~~~~~~~~~~~~
MNR.cpp:1614:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
1614 | for(int iS = 0; iS < S.size(); ++iS){
| ~~~^~~~~~~~~~
MNR.cpp:1695:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
1695 | for(int iRow = 0; iRow < lambdaProv.n_rows; ++iRow){
| ~~~~~^~~~~~~~~~~~~~~~~~~
MNR.cpp:1696:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
1696 | for(int iCol = 0; iCol < lambdaProv.n_cols; ++iCol){
| ~~~~~^~~~~~~~~~~~~~~~~~~
MNR.cpp:1722:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
1722 | for(int iS = 0; iS < S.size(); ++iS){ // Rij <- S[[iS]]%*%Ri
| ~~~^~~~~~~~~~
MNR.cpp:1780:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
1780 | for(int i = 0; i < thetaCUnlisted.size() ; ++i){
| ~~^~~~~~~~~~~~~~~~~~~~~~~
MNR.cpp:1787:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
1787 | for(int j = 0; j < toBoundary.n_cols ; ++j){
| ~~^~~~~~~~~~~~~~~~~~~
MNR.cpp:1528:10: warning: unused variable ‘ok’ [-Wunused-variable]
1528 | bool ok = log_det(val, sign, theta(nRRe-1)); // form 2
| ^~
MNR.cpp: In function ‘arma::vec varCols(const arma::mat&)’:
MNR.cpp:148:19: warning: ‘n’ may be used uninitialized [-Wmaybe-uninitialized]
148 | out(j) = M2/(n-1);
| ~~^~~
MNR.cpp:138:9: note: ‘n’ was declared here
138 | int n;
| ^
MNR.cpp: In function ‘Rcpp::List ai_mme_sp(const arma::sp_mat&, const Rcpp::List&, const arma::vec&, const Rcpp::List&, const arma::sp_mat&, const Rcpp::List&, const Rcpp::List&, const arma::sp_mat&, const bool&, int, double, double, double, const Rcpp::List&, const Rcpp::List&, const arma::mat&, const arma::vec&, const arma::vec&, const arma::vec&, const bool&)’:
MNR.cpp:1286:37: warning: ‘nRe’ may be used uninitialized [-Wmaybe-uninitialized]
1286 | arma::field<arma::sp_mat> Ai(nReAl); // allocate size of Ai field
| ^
MNR.cpp:1245:7: note: ‘nRe’ was declared here
1245 | int nRe;
| ^~~
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::mat&, const bool&, int, double, double, const bool&, const bool&, const bool&, const bool&, const arma::vec&, const arma::vec&)’:
MNR.cpp:1108:36: warning: ‘cycle2’ may be used uninitialized [-Wmaybe-uninitialized]
1108 | arma::mat monitor2 = monitor.cols(0, cycle2);
| ~~~~~~~~~~~~^~~~~~~~~~~
MNR.cpp:719:14: note: ‘cycle2’ was declared here
719 | int cycle, cycle2, ikk;
| ^~~~~~
MNR.cpp:1099:20: warning: ‘llik’ may be used uninitialized [-Wmaybe-uninitialized]
1099 | double AIC = (-2 * llik) + (2 * Xm.n_cols);
| ~~~~^~~~~~~
MNR.cpp:720:16: note: ‘llik’ was declared here
720 | double ldet, llik, llik0, delta_llik, checkP, seconds; // to store likelihoods and determinants
| ^~~~
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'/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++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o sommer.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/RtmpPcNQq1/R.INSTALL29f14a6aeddcba/sommer/src'
make[1]: Entering directory '/tmp/RtmpPcNQq1/R.INSTALL29f14a6aeddcba/sommer/src'
make[1]: Leaving directory '/tmp/RtmpPcNQq1/R.INSTALL29f14a6aeddcba/sommer/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-sommer/00new/sommer/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘sommer’
finding HTML links ... done
A.mat html
AI html
AR1mat html
ARMAmat html
CSmat html
D.mat html
DT_augment html
DT_btdata html
DT_cornhybrids html
DT_cpdata html
DT_example html
DT_expdesigns html
DT_fulldiallel html
DT_gryphon html
DT_h2 html
DT_halfdiallel html
DT_ige html
DT_legendre html
DT_mohring html
DT_polyploid html
DT_rice html
DT_sleepstudy html
DT_technow html
DT_wheat html
DT_yatesoats html
E.mat html
EM html
EMMA html
GWAS html
H.mat html
LD.decay html
add.diallel.vars html
adiag1 html
anova_mmec html
anova_mmer html
atc html
atcg1234 html
atcg1234BackTransform html
atr html
bathy.colors html
bbasis html
bivariateRun html
build.HMM html
coef_mmec html
coef_mmer html
corImputation html
covc html
csc html
csr html
dfToMatrix html
dsc html
dsr html
fcm html
fitted_mmec html
fitted_mmer html
fixm html
gvsr html
impute html
isc html
jet.colors html
leg html
list2usmat html
logspace html
manhattan html
map.plot html
mmec html
mmer html
neMarker html
overlay html
plot.monitor html
plot_mmec html
plot_mmer html
predict_mmec html
predict_mmer html
propMissing html
r2 html
randef html
redmm html
residuals_mmec html
residuals_mmer html
rrc html
simGECorMat html
sommer-package html
spl2Da html
spl2Db html
spl2Dc html
spl2Dmats html
stackTrait html
summary_mmec html
summary_mmer html
tpsmmbwrapper html
transformConstraints html
transp html
unsm html
usc html
usr html
vpredict html
vs html
vsc html
vsr html
wald html
*** copying figures
** building package indices
** installing vignettes
** 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 (sommer)