* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘seqtrie’ ...
** package ‘seqtrie’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpUpYqNi/R.INSTALL21cd9725e23fc8/seqtrie/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -I../inst/include -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/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CharCounter.cpp -o CharCounter.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -I../inst/include -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/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RadixForest.cpp -o RadixForest.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -I../inst/include -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/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RadixTree.cpp -o RadixTree.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -I../inst/include -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/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -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 -DRCPP_USE_UNWIND_PROTECT -I. -I../inst/include -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/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pairwise.cpp -o pairwise.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/mpl/apply.hpp:24,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/serialization/array_optimization.hpp:18,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/serialization/array_wrapper.hpp:21,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/serialization/array.hpp:26,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/numeric/ublas/storage.hpp:22,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/numeric/ublas/vector.hpp:21,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/numeric/ublas/matrix.hpp:18,
from ../inst/include/pairwise/pairwise.h:23,
from pairwise.cpp:11:
/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 | );
| ~
| -
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/numeric/ublas/traits.hpp:21,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/numeric/ublas/storage.hpp:27:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/numeric/ublas/detail/iterator.hpp:111:21: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
111 | public std::iterator<IC, T> {
| ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
from /usr/include/c++/13/bits/specfun.h:43,
from /usr/include/c++/13/cmath:3699,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/platform/compiler.h:100,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/r/headers.h:62,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/RcppCommon.h:30,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp.h:27,
from pairwise.cpp:1:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/numeric/ublas/detail/iterator.hpp:149:21: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
149 | public std::iterator<IC, T> {
| ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
204 | public std::iterator<IC, T> {
| ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o seqtrie.so CharCounter.o RadixForest.o RadixTree.o RcppExports.o pairwise.o -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpUpYqNi/R.INSTALL21cd9725e23fc8/seqtrie/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpUpYqNi/R.INSTALL21cd9725e23fc8/seqtrie/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpUpYqNi/R.INSTALL21cd9725e23fc8/seqtrie/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-seqtrie/00new/seqtrie/libs
** R
** data
*** moving datasets to lazyload DB
** 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
* creating tarball
packaged installation of ‘seqtrie’ as ‘seqtrie_0.2.6_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (seqtrie)