Install log for 'pedmod'

* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘pedmod’ ...
** package ‘pedmod’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-23) 13.2.0’
using Fortran compiler: ‘GNU Fortran (Debian 13.2.0-23) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
using C++17
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpfL43Iy/R.INSTALL2b35e52eb52bdb/pedmod/src'
gcc-13 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/testthat/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/psqn/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c C_FORTRAN_interface.c -o C_FORTRAN_interface.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/testthat/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/psqn/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 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/testthat/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/psqn/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c cdfaprx.cpp -o cdfaprx.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/testthat/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/psqn/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c find-tilting-param.cpp -o find-tilting-param.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/testthat/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/psqn/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c graph-partitioning.cpp -o graph-partitioning.o
gfortran-13  -fpic  -g -O2 -Wall -mtune=native  -c mvt.f -o mvt.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/testthat/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/psqn/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c norm-cdf-approx.cpp -o norm-cdf-approx.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/testthat/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/psqn/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c pedigree-ll.cpp -o pedigree-ll.o
gcc-13 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/testthat/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/psqn/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c qnorm.c -o qnorm.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/testthat/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/psqn/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c qtnorm.cpp -o qtnorm.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/testthat/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/psqn/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c r-api.cpp -o r-api.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/testthat/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/psqn/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c sobol.cpp -o sobol.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/testthat/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/psqn/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c test-cdfaprx.cpp -o test-cdfaprx.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/testthat/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/psqn/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c test-find-tilting-param.cpp -o test-find-tilting-param.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/testthat/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/psqn/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c test-pedigree-ll.cpp -o test-pedigree-ll.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/testthat/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/psqn/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c test-qtnorm.cpp -o test-qtnorm.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/testthat/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/psqn/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c test-runner.cpp -o test-runner.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/testthat/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/psqn/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native   -c threat-safe-random.cpp -o threat-safe-random.o
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/arg.hpp:25,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_concepts.hpp:10,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/range/concepts.hpp:20,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/range/size_type.hpp:20,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/range/size.hpp:21,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/random/hyperexponential_distribution.hpp:29,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/random.hpp:70,
                 from threat-safe-random.cpp:13:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o pedmod.so C_FORTRAN_interface.o RcppExports.o cdfaprx.o find-tilting-param.o graph-partitioning.o mvt.o norm-cdf-approx.o pedigree-ll.o qnorm.o qtnorm.o r-api.o sobol.o test-cdfaprx.o test-find-tilting-param.o test-pedigree-ll.o test-qtnorm.o test-runner.o threat-safe-random.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpfL43Iy/R.INSTALL2b35e52eb52bdb/pedmod/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpfL43Iy/R.INSTALL2b35e52eb52bdb/pedmod/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpfL43Iy/R.INSTALL2b35e52eb52bdb/pedmod/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-pedmod/00new/pedmod/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (pedmod)