* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘Riemann’ ...
** package ‘Riemann’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
using C++11
make[1]: Entering directory '/tmp/Rtmpe11ORo/R.INSTALL1a14366434913b/Riemann/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/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 -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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c auxiliary.cpp -o auxiliary.o
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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c distribution_grassmann.cpp -o distribution_grassmann.o
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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c distribution_sphere.cpp -o distribution_sphere.o
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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c distribution_spnorm.cpp -o distribution_spnorm.o
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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c functions_01_basic.cpp -o functions_01_basic.o
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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c functions_02_inference.cpp -o functions_02_inference.o
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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c functions_03_clustering.cpp -o functions_03_clustering.o
functions_03_clustering.cpp: In function ‘arma::uvec helper_kmeans_initlabel(std::string, arma::cube, int)’:
functions_03_clustering.cpp:94:7: warning: unused variable ‘nrow’ [-Wunused-variable]
94 | int nrow = data.n_rows;
| ^~~~
functions_03_clustering.cpp:95:7: warning: unused variable ‘ncol’ [-Wunused-variable]
95 | int ncol = data.n_cols;
| ^~~~
functions_03_clustering.cpp:102:8: warning: unused variable ‘status’ [-Wunused-variable]
102 | bool status = arma::kmeans(means, arma::trans(logvecs), K, random_subset, 50, false);
| ^~~~~~
functions_03_clustering.cpp: In function ‘arma::cube clustering_kmeans18B_kcenters(std::string, std::string, arma::cube, int)’:
functions_03_clustering.cpp:596:7: warning: unused variable ‘M’ [-Wunused-variable]
596 | int M = data.n_slices;
| ^
functions_03_clustering.cpp:597:7: warning: unused variable ‘nrow’ [-Wunused-variable]
597 | int nrow = data.n_rows;
| ^~~~
functions_03_clustering.cpp:598:7: warning: unused variable ‘ncol’ [-Wunused-variable]
598 | int ncol = data.n_cols;
| ^~~~
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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c functions_03_clustering_criteria.cpp -o functions_03_clustering_criteria.o
functions_03_clustering_criteria.cpp: In function ‘arma::field<arma::Col<unsigned int> > cvi_helper_classindex(arma::uvec)’:
functions_03_clustering_criteria.cpp:27:7: warning: unused variable ‘N’ [-Wunused-variable]
27 | int N = label.n_elem;
| ^
functions_03_clustering_criteria.cpp: In function ‘arma::cube cvi_helper_classmean(std::string, std::string, arma::cube, arma::uvec)’:
functions_03_clustering_criteria.cpp:39:7: warning: unused variable ‘N’ [-Wunused-variable]
39 | int N = X.n_slices;
| ^
functions_03_clustering_criteria.cpp: In function ‘arma::mat cvi_helper_pdist(std::string, std::string, arma::cube)’:
functions_03_clustering_criteria.cpp:57:7: warning: unused variable ‘nrow’ [-Wunused-variable]
57 | int nrow = X.n_rows;
| ^~~~
functions_03_clustering_criteria.cpp:58:7: warning: unused variable ‘ncol’ [-Wunused-variable]
58 | int ncol = X.n_cols;
| ^~~~
functions_03_clustering_criteria.cpp: In function ‘double cvi_internal_db(std::string, std::string, Rcpp::List&, arma::uvec)’:
functions_03_clustering_criteria.cpp:246:7: warning: unused variable ‘Nw’ [-Wunused-variable]
246 | int Nw = cvi_helper_nw(label);
| ^~
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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c functions_05_visualization.cpp -o functions_05_visualization.o
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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c functions_06_curve.cpp -o functions_06_curve.o
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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c functions_07_learning.cpp -o functions_07_learning.o
functions_07_learning.cpp: In function ‘arma::mat alg_GMMLreg(arma::mat, arma::uvec, double)’:
functions_07_learning.cpp:136:30: warning: comparison of integer expressions of different signedness: ‘arma::enable_if2<true, unsigned int>::result’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
136 | if (arma::rank(check_Slbd) < p){
| ~~~~~~~~~~~~~~~~~~~~~~~^~~
functions_07_learning.cpp:124:7: warning: unused variable ‘n’ [-Wunused-variable]
124 | int n = X.n_rows;
| ^
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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c functions_special_others.cpp -o functions_special_others.o
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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c functions_special_spd.cpp -o functions_special_spd.o
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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c riemann_general.cpp -o riemann_general.o
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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c riemann_src.cpp -o riemann_src.o
In file included from riemann_src.cpp:3:
riemann_manifolds.h: In function ‘arma::mat correlation_log(arma::mat, arma::mat)’:
riemann_manifolds.h:234:7: warning: unused variable ‘p’ [-Wunused-variable]
234 | int p = X.n_rows;
| ^
riemann_manifolds.h: In function ‘arma::mat stiefel_exp(arma::mat, arma::mat, double)’:
riemann_manifolds.h:259:13: warning: unused variable ‘n’ [-Wunused-variable]
259 | const int n = x.n_rows;
| ^
riemann_manifolds.h: In function ‘arma::mat stiefel_log(arma::mat, arma::mat)’:
riemann_manifolds.h:278:13: warning: unused variable ‘n’ [-Wunused-variable]
278 | const int n = U0.n_rows;
| ^
riemann_manifolds.h: In function ‘double grassmann_dist(arma::mat, arma::mat)’:
riemann_manifolds.h:370:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
370 | for (int i=0;i<s.n_elem;i++){
| ~^~~~~~~~~
riemann_manifolds.h:378:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
378 | for (int i=0;i<s.n_elem;i++){
| ~^~~~~~~~~
riemann_manifolds.h: In function ‘arma::mat grassmann_exp(arma::mat, arma::mat, double)’:
riemann_manifolds.h:390:13: warning: unused variable ‘n’ [-Wunused-variable]
390 | const int n = x.n_rows;
| ^
riemann_manifolds.h:391:13: warning: unused variable ‘p’ [-Wunused-variable]
391 | const int p = x.n_cols;
| ^
riemann_manifolds.h: In function ‘arma::mat grassmann_log(arma::mat, arma::mat)’:
riemann_manifolds.h:407:7: warning: unused variable ‘n’ [-Wunused-variable]
407 | int n = x.n_rows;
| ^
riemann_src.cpp: In function ‘arma::mat internal_logvectors(std::string, arma::cube)’:
riemann_src.cpp:343:7: warning: unused variable ‘nrow’ [-Wunused-variable]
343 | int nrow = data.n_rows;
| ^~~~
riemann_src.cpp:344:7: warning: unused variable ‘ncol’ [-Wunused-variable]
344 | int ncol = data.n_cols;
| ^~~~
g++-13 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o Riemann.so RcppExports.o auxiliary.o distribution_grassmann.o distribution_sphere.o distribution_spnorm.o functions_01_basic.o functions_02_inference.o functions_03_clustering.o functions_03_clustering_criteria.o functions_05_visualization.o functions_06_curve.o functions_07_learning.o functions_special_others.o functions_special_spd.o riemann_general.o riemann_src.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/Rtmpe11ORo/R.INSTALL1a14366434913b/Riemann/src'
make[1]: Entering directory '/tmp/Rtmpe11ORo/R.INSTALL1a14366434913b/Riemann/src'
make[1]: Leaving directory '/tmp/Rtmpe11ORo/R.INSTALL1a14366434913b/Riemann/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Riemann/00new/Riemann/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 ‘Riemann’
finding HTML links ... done
ERP html
acg html
cities html
density html
gorilla html
grassmann.optmacg html
grassmann.runif html
grassmann.utest html
hands html
label html
loglkd html
macg html
moSL html
moSN html
orbital html
passiflora html
predict.m2skreg html
riem.clrq html
riem.coreset18B html
riem.distlp html
riem.dtw html
riem.fanova html
riem.hclust html
riem.interp html
riem.interps html
riem.isomap html
riem.kmeans html
riem.kmeans18B html
riem.kmeanspp html
riem.kmedoids html
riem.knn html
riem.kpca html
riem.m2skreg html
riem.m2skregCV html
riem.mds html
riem.mean html
riem.median html
riem.nmshift html
riem.pdist html
riem.pdist2 html
riem.pga html
riem.phate html
riem.rmml html
riem.sammon html
riem.sc05Z html
riem.scNJW html
riem.scSM html
riem.scUL html
riem.seb html
riem.test2bg14 html
riem.test2wass html
riem.tsne html
riem.wasserstein html
rmvnorm html
spd.geometry html
spd.pdist html
spd.wassbary html
sphere.convert html
sphere.runif html
sphere.utest html
splaplace html
spnorm html
stiefel.optSA html
stiefel.runif html
stiefel.utest html
wrap.correlation html
wrap.euclidean html
wrap.grassmann html
wrap.landmark html
wrap.multinomial html
wrap.rotation html
wrap.spd html
wrap.spdk html
wrap.sphere html
wrap.stiefel 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 (Riemann)