* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘funMoDisco’ ...
** this is package ‘funMoDisco’ version ‘1.0.0’
** package ‘funMoDisco’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-8) 14.3.0’
using C++20
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpdUDfen/R.INSTALLe0211251f1774/funMoDisco/src'
g++-14 -std=gnu++20 -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 -I./include -fpic -g -O2 -Wall -pedantic -mtune=native -c DissimilarityH1.cpp -o DissimilarityH1.o
g++-14 -std=gnu++20 -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 -I./include -fpic -g -O2 -Wall -pedantic -mtune=native -c DissimilarityL2.cpp -o DissimilarityL2.o
g++-14 -std=gnu++20 -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 -I./include -fpic -g -O2 -Wall -pedantic -mtune=native -c MotifH1.cpp -o MotifH1.o
g++-14 -std=gnu++20 -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 -I./include -fpic -g -O2 -Wall -pedantic -mtune=native -c MotifL2.cpp -o MotifL2.o
g++-14 -std=gnu++20 -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 -I./include -fpic -g -O2 -Wall -pedantic -mtune=native -c MotifSobol.cpp -o MotifSobol.o
g++-14 -std=gnu++20 -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 -I./include -fpic -g -O2 -Wall -pedantic -mtune=native -c Parameters.cpp -o Parameters.o
g++-14 -std=gnu++20 -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 -I./include -fpic -g -O2 -Wall -pedantic -mtune=native -c PerformanceH1.cpp -o PerformanceH1.o
g++-14 -std=gnu++20 -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 -I./include -fpic -g -O2 -Wall -pedantic -mtune=native -c PerformanceL2.cpp -o PerformanceL2.o
g++-14 -std=gnu++20 -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 -I./include -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++20 -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 -I./include -fpic -g -O2 -Wall -pedantic -mtune=native -c SobolDiss.cpp -o SobolDiss.o
SobolDiss.cpp: In member function ‘virtual double SobolDiss::distance(const KMA::matrix&, const KMA::matrix&) const’:
SobolDiss.cpp:16:17: warning: ‘bool arma::is_finite(const Base<typename T1::elem_type, T1>&) [with T1 = subview<double>; typename T1::elem_type = double]’ is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations]
16 | if(is_finite(y.row(i))){n_rows += 1;}
| ~~~~~~~~~^~~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:518,
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:32,
from ./include/TypeTraits.hpp:3,
from ./include/Dissimilarity.hpp:3,
from SobolDiss.cpp:1:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:181:1: note: declared here
181 | is_finite(const Base<typename T1::elem_type,T1>& X)
| ^~~~~~~~~
g++-14 -std=gnu++20 -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 -I./include -fpic -g -O2 -Wall -pedantic -mtune=native -c probKMAImpl.cpp -o probKMAImpl.o
probKMAImpl.cpp: In member function ‘Rcpp::List ProbKMA::_probKMAImp::compute_silhouette(bool)’:
probKMAImpl.cpp:749:28: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
749 | if(!arma::is_finite(sil))
| ~~~~~~~~~~~~~~~^~~~~
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:518,
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:32,
from ./include/ProbKMA.hpp:4,
from probKMAImpl.cpp:1:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
| ^~~~~~~~~
g++-14 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o funMoDisco.so DissimilarityH1.o DissimilarityL2.o MotifH1.o MotifL2.o MotifSobol.o Parameters.o PerformanceH1.o PerformanceL2.o RcppExports.o SobolDiss.o probKMAImpl.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/RtmpdUDfen/R.INSTALLe0211251f1774/funMoDisco/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpdUDfen/R.INSTALLe0211251f1774/funMoDisco/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpdUDfen/R.INSTALLe0211251f1774/funMoDisco/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-funMoDisco/00new/funMoDisco/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 ‘funMoDisco’
finding HTML links ... done
ProbKMA html
add_error_to_motif html
add_motif html
cluster_candidate_motifs html
cluster_candidate_motifs_plot html
compare_nodes html
discoverMotifs html
dot-check_fits html
dot-diss_d0_d1_L2 html
dot-domain html
dot-find_min_diss html
dot-find_occurrences html
dot-generate_coefficients html
dot-mapply_custom html
dot-resample html
dot-select_domain html
dot-transform_list html
dot-transform_to_matrix html
filter_candidate_motifs html
find_recommended_path html
funMoDisco-package html
generateCurves-motifSimulation-method html
generateCurves html
generate_background_curve html
generate_curve_vector html
get_accolites html
get_minidend html
get_parents html
get_path_complete html
initialChecks html
motifSimulation-class html
motifSimulationApp html
motifSimulationBuilder html
motifs_search html
motifs_search_plot html
padding html
plot_motifs-motifSimulation-method html
plot_motifs html
probKMA_plot html
probKMA_silhouette_filter html
probKMA_silhouette_plot html
probKMA_wrap html
recommend_node html
simulated200 html
simulatedHighDimensional html
to_motifDiscovery-list-method html
to_motifDiscovery html
** 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 (funMoDisco)