* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘pleiotest’ ...
** this is package ‘pleiotest’ version ‘1.0.0’
** package ‘pleiotest’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-10) 14.3.0’
using C++11
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpZxqd4q/R.INSTALL1587a76aa6baeb/pleiotest/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/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c PleioSeqTestc.cpp -o PleioSeqTestc.o
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/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 -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 getXX_XYc.cpp -o getXX_XYc.o
getXX_XYc.cpp: In function ‘Rcpp::List getXX_XYc(Rcpp::IntegerVector, Rcpp::List, Rcpp::List, Rcpp::IntegerMatrix, Rcpp::List)’:
getXX_XYc.cpp:26:25: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = int; typename arma_scalar_only<eT>::result = int]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
   26 |       if(arma::is_finite(x_i[j])){
      |          ~~~~~~~~~~~~~~~^~~~~~~~
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 getXX_XYc.cpp:2:
/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)
      | ^~~~~~~~~
getXX_XYc.cpp:52:25: 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]
   52 |       if(arma::is_finite(res)){
      |          ~~~~~~~~~~~~~~~^~~~~
/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++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o pleiotest.so PleioSeqTestc.o RcppExports.o getXX_XYc.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/RtmpZxqd4q/R.INSTALL1587a76aa6baeb/pleiotest/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpZxqd4q/R.INSTALL1587a76aa6baeb/pleiotest/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpZxqd4q/R.INSTALL1587a76aa6baeb/pleiotest/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-pleiotest/00new/pleiotest/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘pleiotest’
    finding HTML links ... done
    identify_subsets                        html  
    manhattan_plot                          html  
    mt_gwas                                 html  
    pleioR                                  html  
    pleio_ideogram                          html  
    pleio_plot                              html  
    pleio_simulate                          html  
    pleio_test                              html  
    xrsx_xrsy                               html  
*** copying figures
** 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 (pleiotest)