* installing *source* package ‘dynsurv’ ...
** package ‘dynsurv’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 18.1.4’
using C++ compiler: ‘clang version 18.1.4’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/dynsurv/src'
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DNDEBUG -DBOOST_NO_AUTO_PTR -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include   -I. -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c IntRegPar.cpp -o IntRegPar.o
In file included from IntRegPar.cpp:10:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:20:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/config.hpp:48:
/data/gannet/ripley/R/test-clang/BH/include/boost/config/stdlib/libcpp.hpp:98:11: warning: 'BOOST_NO_AUTO_PTR' macro redefined [-Wmacro-redefined]
   98 | #  define BOOST_NO_AUTO_PTR
      |           ^
<command line>:3:9: note: previous definition is here
    3 | #define BOOST_NO_AUTO_PTR 1
      |         ^
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DNDEBUG -DBOOST_NO_AUTO_PTR -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c arms.c -o arms.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DNDEBUG -DBOOST_NO_AUTO_PTR -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include   -I. -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c bayesCox.cpp -o bayesCox.o
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:20:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/config.hpp:48:
/data/gannet/ripley/R/test-clang/BH/include/boost/config/stdlib/libcpp.hpp:98:11: warning: 'BOOST_NO_AUTO_PTR' macro redefined [-Wmacro-redefined]
   98 | #  define BOOST_NO_AUTO_PTR
      |           ^
<command line>:3:9: note: previous definition is here
    3 | #define BOOST_NO_AUTO_PTR 1
      |         ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:17:
./TimeIndepModel.h:65:7: warning: variable 'err' set but not used [-Wunused-but-set-variable]
   65 |   int err;
      |       ^
In file included from bayesCox.cpp:4:
In file included from ./TimeVaryingCoxModel.h:17:
./TimeVaryingModel.h:85:7: warning: variable 'err' set but not used [-Wunused-but-set-variable]
   85 |   int err;
      |       ^
./TimeVaryingModel.h:162:7: warning: variable 'err' set but not used [-Wunused-but-set-variable]
  162 |   int err;
      |       ^
In file included from bayesCox.cpp:5:
In file included from ./DynamicCoxModel.h:17:
./DynamicModel.h:355:11: warning: variable 'err' set but not used [-Wunused-but-set-variable]
  355 |       int err;
      |           ^
./DynamicModel.h:452:11: warning: variable 'err' set but not used [-Wunused-but-set-variable]
  452 |       int err;
      |           ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:518:18: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::vector<double>::const_iterator, double>' requested here
  518 |                  public random_access_iterator_base<dense_random_access_iterator_tag,
      |                         ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::vector<double>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:385:11: note: in instantiation of function template specialization 'boost::numeric::ublas::vector_assign<boost::numeric::ublas::scalar_plus_assign, boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>>' requested here
  385 |                  vector_assign<scalar_plus_assign> (*this, ae);
      |                  ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:372:11: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::plus_assign<boost::numeric::ublas::vector<double>>' requested here
  372 |                  plus_assign (v);
      |                  ^
./IntRegPar.h:147:16: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::operator+=<boost::numeric::ublas::vector<double>>' requested here
  147 |     par.lambda += vp[i].lambda;
      |                ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:486:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix<double>::const_iterator1, double>' requested here
  486 |             public random_access_iterator_base<dense_random_access_iterator_tag,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1364:59: note: in instantiation of member class 'boost::numeric::ublas::matrix<double>::const_iterator1' requested here
 1364 |                                               typename E::const_iterator1::iterator_category,
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:377:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_plus_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>>' requested here
  377 |             matrix_assign<scalar_plus_assign> (*this, ae);
      |             ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:371:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::plus_assign<boost::numeric::ublas::matrix<double>>' requested here
  371 |             plus_assign (m);
      |             ^
./IntRegPar.h:195:14: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::operator+=<boost::numeric::ublas::matrix<double>>' requested here
  195 |     par.beta += vp[i].beta;
      |              ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:809:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix<double>::const_iterator2, double>' requested here
  809 |             public random_access_iterator_base<dense_random_access_iterator_tag,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1365:59: note: in instantiation of member class 'boost::numeric::ublas::matrix<double>::const_iterator2' requested here
 1365 |                                               typename E::const_iterator2::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:377:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_plus_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>>' requested here
  377 |             matrix_assign<scalar_plus_assign> (*this, ae);
      |             ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:371:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::plus_assign<boost::numeric::ublas::matrix<double>>' requested here
  371 |             plus_assign (m);
      |             ^
./IntRegPar.h:195:14: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::operator+=<boost::numeric::ublas::matrix<double>>' requested here
  195 |     par.beta += vp[i].beta;
      |              ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:486:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix<int>::const_iterator1, int>' requested here
  486 |             public random_access_iterator_base<dense_random_access_iterator_tag,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1364:59: note: in instantiation of member class 'boost::numeric::ublas::matrix<int>::const_iterator1' requested here
 1364 |                                               typename E::const_iterator1::iterator_category,
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:377:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_plus_assign, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix<int>>' requested here
  377 |             matrix_assign<scalar_plus_assign> (*this, ae);
      |             ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:371:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<int>::plus_assign<boost::numeric::ublas::matrix<int>>' requested here
  371 |             plus_assign (m);
      |             ^
./IntRegPar.h:235:14: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<int>::operator+=<boost::numeric::ublas::matrix<int>>' requested here
  235 |     par.jump += vp[i].jump;
      |              ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:809:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix<int>::const_iterator2, int>' requested here
  809 |             public random_access_iterator_base<dense_random_access_iterator_tag,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1365:59: note: in instantiation of member class 'boost::numeric::ublas::matrix<int>::const_iterator2' requested here
 1365 |                                               typename E::const_iterator2::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:377:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_plus_assign, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix<int>>' requested here
  377 |             matrix_assign<scalar_plus_assign> (*this, ae);
      |             ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:371:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<int>::plus_assign<boost::numeric::ublas::matrix<int>>' requested here
  371 |             plus_assign (m);
      |             ^
./IntRegPar.h:235:14: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<int>::operator+=<boost::numeric::ublas::matrix<int>>' requested here
  235 |     par.jump += vp[i].jump;
      |              ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_proxy.hpp:2664:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<double>>::const_iterator1, double>' requested here
 2664 |             public iterator_base_traits<typename const_subiterator1_type::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1364:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<double>>::const_iterator1' requested here
 1364 |                                               typename E::const_iterator1::iterator_category,
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./IntRegData.h:25:7: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<double>>>' requested here
   25 |     : X_  (ublas::subrange(LRX, 0, LRX.size1(), 2, LRX.size2())),
      |       ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_proxy.hpp:2975:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<double>>::const_iterator2, double>' requested here
 2975 |             public iterator_base_traits<typename const_subiterator2_type::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1365:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<double>>::const_iterator2' requested here
 1365 |                                               typename E::const_iterator2::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./IntRegData.h:25:7: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<double>>>' requested here
   25 |     : X_  (ublas::subrange(LRX, 0, LRX.size1(), 2, LRX.size2())),
      |       ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_proxy.hpp:714:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>::const_iterator, double>' requested here
  714 |             public iterator_base_traits<typename const_subiterator_type::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:131:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::vector<double>, boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>>' requested here
  131 |                 vector_assign<scalar_assign> (*this, ae);
      |                 ^
./IntRegData.h:27:7: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::vector<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>>' requested here
   27 |       left_ (ublas::column(LRX, 0)),
      |       ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:460:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::vector_matrix_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_multiplies<double, double>>::const_iterator1, double>' requested here
  460 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1364:59: note: in instantiation of member class 'boost::numeric::ublas::vector_matrix_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_multiplies<double, double>>::const_iterator1' requested here
 1364 |                                               typename E::const_iterator1::iterator_category,
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::vector_matrix_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_multiplies<double, double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./TimeIndepCoxModel.h:64:25: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::vector_matrix_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_multiplies<double, double>>>' requested here
   64 |   ublas::matrix<double> tBetaMat(ublas::outer_prod(par.beta,
      |                         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:661:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::vector_matrix_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_multiplies<double, double>>::const_iterator2, double>' requested here
  661 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1365:59: note: in instantiation of member class 'boost::numeric::ublas::vector_matrix_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_multiplies<double, double>>::const_iterator2' requested here
 1365 |                                               typename E::const_iterator2::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::vector_matrix_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_multiplies<double, double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./TimeIndepCoxModel.h:64:25: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::vector_matrix_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_multiplies<double, double>>>' requested here
   64 |   ublas::matrix<double> tBetaMat(ublas::outer_prod(par.beta,
      |                         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:4961:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, double>>::const_iterator1, double>' requested here
 4961 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator1::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1034:46: note: in instantiation of member class 'boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, double>>::const_iterator1' requested here
 1034 |             public iterator_base_traits<typename E::const_iterator1::iterator_category>::template
      |                                                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1364:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator1' requested here
 1364 |                                               typename E::const_iterator1::iterator_category,
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./TimeIndepCoxModel.h:66:25: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
   66 |   ublas::matrix<double> expXb(ublas::exp(ublas::prod(this->pd_->X(), tBetaMat)));
      |                         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1034:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator1, double>' requested here
 1034 |             public iterator_base_traits<typename E::const_iterator1::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1364:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator1' requested here
 1364 |                                               typename E::const_iterator1::iterator_category,
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./TimeIndepCoxModel.h:66:25: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
   66 |   ublas::matrix<double> expXb(ublas::exp(ublas::prod(this->pd_->X(), tBetaMat)));
      |                         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:5223:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, double>>::const_iterator2, double>' requested here
 5223 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator1::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1205:46: note: in instantiation of member class 'boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, double>>::const_iterator2' requested here
 1205 |             public iterator_base_traits<typename E::const_iterator2::iterator_category>::template
      |                                                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1365:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator2' requested here
 1365 |                                               typename E::const_iterator2::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./TimeIndepCoxModel.h:66:25: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
   66 |   ublas::matrix<double> expXb(ublas::exp(ublas::prod(this->pd_->X(), tBetaMat)));
      |                         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1205:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator2, double>' requested here
 1205 |             public iterator_base_traits<typename E::const_iterator2::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1365:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator2' requested here
 1365 |                                               typename E::const_iterator2::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./TimeIndepCoxModel.h:66:25: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
   66 |   ublas::matrix<double> expXb(ublas::exp(ublas::prod(this->pd_->X(), tBetaMat)));
      |                         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:4961:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>::const_iterator1, double>' requested here
 4961 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator1::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1034:46: note: in instantiation of member class 'boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>::const_iterator1' requested here
 1034 |             public iterator_base_traits<typename E::const_iterator1::iterator_category>::template
      |                                                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1034:46: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>::const_iterator1' requested here
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1364:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator1' requested here
 1364 |                                               typename E::const_iterator1::iterator_category,
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./CoxModel.h:80:29: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
   80 |       ublas::matrix<double> survMat(ublas::exp(- ublas::prod(expXbDL,
      |                             ^
./TimeIndepCoxModel.h:71:9: note: in instantiation of member function 'ir::CoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::sampleMat' requested here
   71 |   this->sampleMat(par.lambda, expXb, dNMat, YMat);
      |         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1034:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>::const_iterator1, double>' requested here
 1034 |             public iterator_base_traits<typename E::const_iterator1::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1034:46: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>::const_iterator1' requested here
 1034 |             public iterator_base_traits<typename E::const_iterator1::iterator_category>::template
      |                                                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1364:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator1' requested here
 1364 |                                               typename E::const_iterator1::iterator_category,
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./CoxModel.h:80:29: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
   80 |       ublas::matrix<double> survMat(ublas::exp(- ublas::prod(expXbDL,
      |                             ^
./TimeIndepCoxModel.h:71:9: note: in instantiation of member function 'ir::CoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::sampleMat' requested here
   71 |   this->sampleMat(par.lambda, expXb, dNMat, YMat);
      |         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1034:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator1, double>' requested here
 1034 |             public iterator_base_traits<typename E::const_iterator1::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1364:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator1' requested here
 1364 |                                               typename E::const_iterator1::iterator_category,
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./CoxModel.h:80:29: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
   80 |       ublas::matrix<double> survMat(ublas::exp(- ublas::prod(expXbDL,
      |                             ^
./TimeIndepCoxModel.h:71:9: note: in instantiation of member function 'ir::CoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::sampleMat' requested here
   71 |   this->sampleMat(par.lambda, expXb, dNMat, YMat);
      |         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:5223:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>::const_iterator2, double>' requested here
 5223 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator1::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1205:46: note: in instantiation of member class 'boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>::const_iterator2' requested here
 1205 |             public iterator_base_traits<typename E::const_iterator2::iterator_category>::template
      |                                                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1205:46: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>::const_iterator2' requested here
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1365:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator2' requested here
 1365 |                                               typename E::const_iterator2::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./CoxModel.h:80:29: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
   80 |       ublas::matrix<double> survMat(ublas::exp(- ublas::prod(expXbDL,
      |                             ^
./TimeIndepCoxModel.h:71:9: note: in instantiation of member function 'ir::CoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::sampleMat' requested here
   71 |   this->sampleMat(par.lambda, expXb, dNMat, YMat);
      |         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1205:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>::const_iterator2, double>' requested here
 1205 |             public iterator_base_traits<typename E::const_iterator2::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1205:46: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>::const_iterator2' requested here
 1205 |             public iterator_base_traits<typename E::const_iterator2::iterator_category>::template
      |                                                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1365:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator2' requested here
 1365 |                                               typename E::const_iterator2::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./CoxModel.h:80:29: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
   80 |       ublas::matrix<double> survMat(ublas::exp(- ublas::prod(expXbDL,
      |                             ^
./TimeIndepCoxModel.h:71:9: note: in instantiation of member function 'ir::CoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::sampleMat' requested here
   71 |   this->sampleMat(par.lambda, expXb, dNMat, YMat);
      |         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1205:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator2, double>' requested here
 1205 |             public iterator_base_traits<typename E::const_iterator2::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1365:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator2' requested here
 1365 |                                               typename E::const_iterator2::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./CoxModel.h:80:29: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<int>, double>>, boost::numeric::ublas::scalar_negate<double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
   80 |       ublas::matrix<double> survMat(ublas::exp(- ublas::prod(expXbDL,
      |                             ^
./TimeIndepCoxModel.h:71:9: note: in instantiation of member function 'ir::CoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::sampleMat' requested here
   71 |   this->sampleMat(par.lambda, expXb, dNMat, YMat);
      |         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_proxy.hpp:241:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>::const_iterator, int>' requested here
  241 |             public iterator_base_traits<typename const_subiterator_type::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:4513:81: note: in instantiation of member class 'boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>::const_iterator' requested here
 4513 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator::iterator_category,
      |                                                                                        ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1333:54: note: in instantiation of member class 'boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>::const_iterator' requested here
 1333 |             public iterator_base_traits<typename E1::const_iterator::iterator_category>::template
      |                                                      ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:653:88: note: in instantiation of member class 'boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>::const_iterator' requested here
  653 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator::iterator_category,
      |                                                                                        ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::scalar_plus<int, int>>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:131:10: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
  131 |                 vector_assign<scalar_assign> (*this, ae);
      |                 ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_proxy.hpp:127:50: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::vector<boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::scalar_plus<int, int>>>' requested here
  127 |             vector_assign<scalar_assign> (*this, typename vector_temporary_traits<M>::type (ae));
      |                                                  ^
./CoxModel.h:111:29: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>::operator=<boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::scalar_plus<int, int>>>' requested here
  111 |         ublas::row(YMat, i) = ublas::prod(ublas::row(dNMat, i),
      |                             ^
./TimeIndepCoxModel.h:71:9: note: in instantiation of member function 'ir::CoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::sampleMat' requested here
   71 |   this->sampleMat(par.lambda, expXb, dNMat, YMat);
      |         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1767:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>::const_iterator2, int>' requested here
 1767 |             public iterator_base_traits<typename E::const_iterator1::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:4514:19: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>::const_iterator2' requested here
 4514 |             typename E2::const_iterator2::iterator_category>::iterator_category>::template
      |                          ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1333:54: note: in instantiation of member class 'boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>::const_iterator' requested here
 1333 |             public iterator_base_traits<typename E1::const_iterator::iterator_category>::template
      |                                                      ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:653:88: note: in instantiation of member class 'boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>::const_iterator' requested here
  653 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator::iterator_category,
      |                                                                                        ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::scalar_plus<int, int>>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:131:10: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
  131 |                 vector_assign<scalar_assign> (*this, ae);
      |                 ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_proxy.hpp:127:50: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::vector<boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::scalar_plus<int, int>>>' requested here
  127 |             vector_assign<scalar_assign> (*this, typename vector_temporary_traits<M>::type (ae));
      |                                                  ^
./CoxModel.h:111:29: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>::operator=<boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::scalar_plus<int, int>>>' requested here
  111 |         ublas::row(YMat, i) = ublas::prod(ublas::row(dNMat, i),
      |                             ^
./TimeIndepCoxModel.h:71:9: note: in instantiation of member function 'ir::CoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::sampleMat' requested here
   71 |   this->sampleMat(par.lambda, expXb, dNMat, YMat);
      |         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:4513:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>::const_iterator, int>' requested here
 4513 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1333:54: note: in instantiation of member class 'boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>::const_iterator' requested here
 1333 |             public iterator_base_traits<typename E1::const_iterator::iterator_category>::template
      |                                                      ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:653:88: note: in instantiation of member class 'boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>::const_iterator' requested here
  653 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator::iterator_category,
      |                                                                                        ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::scalar_plus<int, int>>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:131:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::scalar_plus<int, int>>>' requested here
  131 |                 vector_assign<scalar_assign> (*this, ae);
      |                 ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_proxy.hpp:127:50: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::vector<boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::scalar_plus<int, int>>>' requested here
  127 |             vector_assign<scalar_assign> (*this, typename vector_temporary_traits<M>::type (ae));
      |                                                  ^
./CoxModel.h:111:29: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>::operator=<boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::scalar_plus<int, int>>>' requested here
  111 |         ublas::row(YMat, i) = ublas::prod(ublas::row(dNMat, i),
      |                             ^
./TimeIndepCoxModel.h:71:9: note: in instantiation of member function 'ir::CoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::sampleMat' requested here
   71 |   this->sampleMat(par.lambda, expXb, dNMat, YMat);
      |         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1333:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>::const_iterator, int>' requested here
 1333 |             public iterator_base_traits<typename E1::const_iterator::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:653:88: note: in instantiation of member class 'boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>::const_iterator' requested here
  653 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator::iterator_category,
      |                                                                                        ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::scalar_plus<int, int>>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:131:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::scalar_plus<int, int>>>' requested here
  131 |                 vector_assign<scalar_assign> (*this, ae);
      |                 ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_proxy.hpp:127:50: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::vector<boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::scalar_plus<int, int>>>' requested here
  127 |             vector_assign<scalar_assign> (*this, typename vector_temporary_traits<M>::type (ae));
      |                                                  ^
./CoxModel.h:111:29: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>::operator=<boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::scalar_plus<int, int>>>' requested here
  111 |         ublas::row(YMat, i) = ublas::prod(ublas::row(dNMat, i),
      |                             ^
./TimeIndepCoxModel.h:71:9: note: in instantiation of member function 'ir::CoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::sampleMat' requested here
   71 |   this->sampleMat(par.lambda, expXb, dNMat, YMat);
      |         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:653:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::scalar_plus<int, int>>::const_iterator, int>' requested here
  653 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::scalar_plus<int, int>>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:131:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::scalar_plus<int, int>>>' requested here
  131 |                 vector_assign<scalar_assign> (*this, ae);
      |                 ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_proxy.hpp:127:50: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::vector<boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::scalar_plus<int, int>>>' requested here
  127 |             vector_assign<scalar_assign> (*this, typename vector_temporary_traits<M>::type (ae));
      |                                                  ^
./CoxModel.h:111:29: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>::operator=<boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::scalar_identity<int>>, int>>, const int, boost::numeric::ublas::scalar_multiplies<int, int>>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::scalar_plus<int, int>>>' requested here
  111 |         ublas::row(YMat, i) = ublas::prod(ublas::row(dNMat, i),
      |                             ^
./TimeIndepCoxModel.h:71:9: note: in instantiation of member function 'ir::CoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::sampleMat' requested here
   71 |   this->sampleMat(par.lambda, expXb, dNMat, YMat);
      |         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_proxy.hpp:714:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<int>>::const_iterator, int>' requested here
  714 |             public iterator_base_traits<typename const_subiterator_type::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1510:29: note: in instantiation of member class 'boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<int>>::const_iterator' requested here
 1510 |         typedef typename E::const_iterator::iterator_category iterator_category;
      |                             ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1589:16: note: in instantiation of template class 'boost::numeric::ublas::vector_scalar_unary<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::vector_sum<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<int>>>>' requested here
 1589 |         return expression_type (e ());
      |                ^
./CoxModel.h:132:50: note: in instantiation of function template specialization 'boost::numeric::ublas::sum<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<int>>>' requested here
  132 |         double shape = base_prior.shape + ublas::sum(ublas::column(dNMat, k));
      |                                                  ^
./TimeIndepCoxModel.h:74:9: note: in instantiation of member function 'ir::CoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::sampleLambda' requested here
   74 |   this->sampleLambda(expXb, dNMat, YMat, prior.base_prior, par.lambda);
      |         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:653:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_multiplies<double, double>>::const_iterator, double>' requested here
  653 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_multiplies<double, double>>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:131:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_multiplies<double, double>>>' requested here
  131 |                 vector_assign<scalar_assign> (*this, ae);
      |                 ^
./TimeIndepModel.h:67:25: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::vector<boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_multiplies<double, double>>>' requested here
   67 |   ublas::vector<double> DL(ublas::element_prod(this->delta_, lambda));
      |                         ^
./TimeIndepCoxModel.h:78:9: note: in instantiation of member function 'ir::TimeIndepModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::sampleBeta' requested here
   78 |   this->sampleBeta(par.lambda, dNMat, YMat, omega, prior.coef_prior, par.beta);
      |         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:518:18: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::vector<int>::const_iterator, int>' requested here
  518 |                  public random_access_iterator_base<dense_random_access_iterator_tag,
      |                         ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:4108:19: note: in instantiation of member class 'boost::numeric::ublas::vector<int>::const_iterator' requested here
 4108 |             typename E2::const_iterator::iterator_category>::iterator_category>::template
      |                          ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::vector<int>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::vector<int>, int>>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:131:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::vector<int>, boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::vector<int>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::vector<int>, int>>>' requested here
  131 |                 vector_assign<scalar_assign> (*this, ae);
      |                 ^
./ublas_ext.h:115:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<int>::vector<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::vector<int>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::vector<int>, int>>>' requested here
  115 |   return prod(m, vector<int>(m.size2(), 1));
      |          ^
./TimeIndepModel.h:68:41: note: in instantiation of function template specialization 'boost::numeric::ublas::row_sum<int>' requested here
   68 |   ublas::vector<double> dNMat_rs(ublas::row_sum(dNMat));
      |                                         ^
./TimeIndepCoxModel.h:78:9: note: in instantiation of member function 'ir::TimeIndepModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::sampleBeta' requested here
   78 |   this->sampleBeta(par.lambda, dNMat, YMat, omega, prior.coef_prior, par.beta);
      |         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:4107:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::vector<int>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::vector<int>, int>>::const_iterator, int>' requested here
 4107 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator1::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::vector<int>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::vector<int>, int>>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:131:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::vector<int>, boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::vector<int>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::vector<int>, int>>>' requested here
  131 |                 vector_assign<scalar_assign> (*this, ae);
      |                 ^
./ublas_ext.h:115:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<int>::vector<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::vector<int>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::vector<int>, int>>>' requested here
  115 |   return prod(m, vector<int>(m.size2(), 1));
      |          ^
./TimeIndepModel.h:68:41: note: in instantiation of function template specialization 'boost::numeric::ublas::row_sum<int>' requested here
   68 |   ublas::vector<double> dNMat_rs(ublas::row_sum(dNMat));
      |                                         ^
./TimeIndepCoxModel.h:78:9: note: in instantiation of member function 'ir::TimeIndepModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::sampleBeta' requested here
   78 |   this->sampleBeta(par.lambda, dNMat, YMat, omega, prior.coef_prior, par.beta);
      |         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_proxy.hpp:241:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>::const_iterator, double>' requested here
  241 |             public iterator_base_traits<typename const_subiterator_type::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1650:64: note: in instantiation of member class 'boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>::const_iterator' requested here
 1650 |         typedef typename iterator_restrict_traits<typename E1::const_iterator::iterator_category,
      |                                                                ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1744:16: note: in instantiation of template class 'boost::numeric::ublas::vector_scalar_binary<boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector_inner_prod<boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::vector<double>, double>>' requested here
 1744 |         return expression_type (e1 (), e2 ());
      |                ^
./TimeIndepModel.h:85:39: note: in instantiation of function template specialization 'boost::numeric::ublas::inner_prod<boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::vector<double>>' requested here
   85 |       ldp_dleY[i] = omega(i) * ublas::inner_prod(ublas::row(YMat, i), DL) *
      |                                       ^
./TimeIndepCoxModel.h:78:9: note: in instantiation of member function 'ir::TimeIndepModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::sampleBeta' requested here
   78 |   this->sampleBeta(par.lambda, dNMat, YMat, omega, prior.coef_prior, par.beta);
      |         ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::gibbsKernel' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:4107:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, double>>::const_iterator, double>' requested here
 4107 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator1::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:352:53: note: in instantiation of member class 'boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, double>>::const_iterator' requested here
  352 |             public iterator_base_traits<typename E::const_iterator::iterator_category>::template
      |                                                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::vector_unary<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:131:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector_unary<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
  131 |                 vector_assign<scalar_assign> (*this, ae);
      |                 ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:330:21: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::vector<boost::numeric::ublas::vector_unary<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
  330 |                  self_type temporary (ae);
      |                            ^
./CoxModel.h:182:17: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::operator=<boost::numeric::ublas::vector_unary<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
  182 |         expXb_i = ublas::exp(ublas::prod(betaMat,
      |                 ^
./TimeIndepCoxModel.h:88:16: note: in instantiation of member function 'ir::CoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::coxLikeVec' requested here
   88 |   return this->coxLikeVec(par.lambda, betaMat);
      |                ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::likeVec' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:352:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::vector_unary<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator, double>' requested here
  352 |             public iterator_base_traits<typename E::const_iterator::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::vector_unary<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:131:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector_unary<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
  131 |                 vector_assign<scalar_assign> (*this, ae);
      |                 ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:330:21: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::vector<boost::numeric::ublas::vector_unary<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
  330 |                  self_type temporary (ae);
      |                            ^
./CoxModel.h:182:17: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::operator=<boost::numeric::ublas::vector_unary<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_row<const boost::numeric::ublas::matrix<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
  182 |         expXb_i = ublas::exp(ublas::prod(betaMat,
      |                 ^
./TimeIndepCoxModel.h:88:16: note: in instantiation of member function 'ir::CoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::coxLikeVec' requested here
   88 |   return this->coxLikeVec(par.lambda, betaMat);
      |                ^
./TimeIndepCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::likeVec' requested here
   30 |   TimeIndepCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:48:35: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::TimeIndepCoxModel' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:17:
In file included from ./TimeIndepModel.h:15:
In file included from ./IntRegModel.h:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   44 |     delete x;
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>>' requested here
  154 |             boost::checked_delete( p );
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:280:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>>' requested here
  280 |     boost::detail::shared_count( p ).swap( pn );
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:374:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>, ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>>' requested here
  374 |         boost::detail::sp_pointer_construct( this, p, pn );
      |                        ^
bayesCox.cpp:48:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>>::shared_ptr<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>>' requested here
   48 |       boost::shared_ptr<M> pm(new M(pd));
      |                            ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:15:
In file included from ./IntRegPrior.h:14:
In file included from /usr/local/clang18/bin/../include/c++/v1/iostream:43:
In file included from /usr/local/clang18/bin/../include/c++/v1/ios:223:
In file included from /usr/local/clang18/bin/../include/c++/v1/__locale:15:
In file included from /usr/local/clang18/bin/../include/c++/v1/__memory/shared_ptr.h:25:
/usr/local/clang18/bin/../include/c++/v1/__memory/allocator.h:176:81: warning: destructor called on non-final 'ir::TimeIndepCoxPar' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
  176 |   _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_HIDE_FROM_ABI void destroy(pointer __p) { __p->~_Tp(); }
      |                                                                                 ^
/usr/local/clang18/bin/../include/c++/v1/__memory/allocator_traits.h:311:9: note: in instantiation of member function 'std::allocator<ir::TimeIndepCoxPar>::destroy' requested here
  311 |     __a.destroy(__p);
      |         ^
/usr/local/clang18/bin/../include/c++/v1/vector:926:23: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<ir::TimeIndepCoxPar>>::destroy<ir::TimeIndepCoxPar, void>' requested here
  926 |       __alloc_traits::destroy(__alloc(), std::__to_address(--__soon_to_be_end));
      |                       ^
/usr/local/clang18/bin/../include/c++/v1/vector:920:5: note: in instantiation of member function 'std::vector<ir::TimeIndepCoxPar>::__base_destruct_at_end' requested here
  920 |     __base_destruct_at_end(this->__begin_);
      |     ^
/usr/local/clang18/bin/../include/c++/v1/vector:490:16: note: in instantiation of member function 'std::vector<ir::TimeIndepCoxPar>::__clear' requested here
  490 |         __vec_.__clear();
      |                ^
/usr/local/clang18/bin/../include/c++/v1/vector:501:67: note: in instantiation of member function 'std::vector<ir::TimeIndepCoxPar>::__destroy_vector::operator()' requested here
  501 |   _LIBCPP_CONSTEXPR_SINCE_CXX20 _LIBCPP_HIDE_FROM_ABI ~vector() { __destroy_vector (*this)(); }
      |                                                                   ^
./GibbsSampler.h:40:3: note: in instantiation of member function 'std::vector<ir::TimeIndepCoxPar>::~vector' requested here
   40 |   GibbsSampler(const boost::shared_ptr<M>& pm,
      |   ^
bayesCox.cpp:50:23: note: in instantiation of member function 'ir::GibbsSampler<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>>::GibbsSampler' requested here
   50 |       GibbsSampler<M> gs(pm, p_iter[0]);
      |                       ^
/usr/local/clang18/bin/../include/c++/v1/__memory/allocator.h:176:87: note: qualify call to silence this warning
  176 |   _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_HIDE_FROM_ABI void destroy(pointer __p) { __p->~_Tp(); }
      |                                                                                       ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_proxy.hpp:241:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>::const_iterator, double>' requested here
  241 |             public iterator_base_traits<typename const_subiterator_type::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1510:29: note: in instantiation of member class 'boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>::const_iterator' requested here
 1510 |         typedef typename E::const_iterator::iterator_category iterator_category;
      |                             ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1589:16: note: in instantiation of template class 'boost::numeric::ublas::vector_scalar_unary<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::vector_sum<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>>>' requested here
 1589 |         return expression_type (e ());
      |                ^
./IntRegModel.h:162:28: note: in instantiation of function template specialization 'boost::numeric::ublas::sum<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>>' requested here
  162 |     double rowSum = ublas::sum(ublas::row(eMat, i));
      |                            ^
./TimeIndepCoxModel.h:54:32: note: in instantiation of member function 'ir::IntRegModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::initLambda' requested here
   54 |   return TimeIndepCoxPar(this->initLambda(),
      |                                ^
bayesCox.cpp:53:31: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::initPar' requested here
   53 |       TimeIndepCoxPar par(pm->initPar());
      |                               ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:4107:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, double>>::const_iterator, double>' requested here
 4107 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator1::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1333:54: note: in instantiation of member class 'boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, double>>::const_iterator' requested here
 1333 |             public iterator_base_traits<typename E1::const_iterator::iterator_category>::template
      |                                                      ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:654:88: note: in instantiation of member class 'boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, double>>, const int, boost::numeric::ublas::scalar_multiplies<double, int>>::const_iterator' requested here
  654 |                                                                           typename E2::const_iterator::iterator_category>::iterator_category>::template
      |                                                                                        ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::vector_binary<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, double>>, const int, boost::numeric::ublas::scalar_multiplies<double, int>>, boost::numeric::ublas::scalar_plus<double, double>>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:131:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector_binary<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, double>>, const int, boost::numeric::ublas::scalar_multiplies<double, int>>, boost::numeric::ublas::scalar_plus<double, double>>>' requested here
  131 |                 vector_assign<scalar_assign> (*this, ae);
      |                 ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_proxy.hpp:139:50: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::vector<boost::numeric::ublas::vector_binary<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, double>>, const int, boost::numeric::ublas::scalar_multiplies<double, int>>, boost::numeric::ublas::scalar_plus<double, double>>>' requested here
  139 |             vector_assign<scalar_assign> (*this, typename vector_temporary_traits<M>::type (*this + ae));
      |                                                  ^
./IntRegModel.h:167:25: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>::operator+=<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, double>>, const int, boost::numeric::ublas::scalar_multiplies<double, int>>>' requested here
  167 |     ublas::row(rMat, i) += ublas::prod(csMat_, ublas::row(eMat, i)) *
      |                         ^
./TimeIndepCoxModel.h:54:32: note: in instantiation of member function 'ir::IntRegModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::initLambda' requested here
   54 |   return TimeIndepCoxPar(this->initLambda(),
      |                                ^
bayesCox.cpp:53:31: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::initPar' requested here
   53 |       TimeIndepCoxPar par(pm->initPar());
      |                               ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1333:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, double>>, const int, boost::numeric::ublas::scalar_multiplies<double, int>>::const_iterator, double>' requested here
 1333 |             public iterator_base_traits<typename E1::const_iterator::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:654:88: note: in instantiation of member class 'boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, double>>, const int, boost::numeric::ublas::scalar_multiplies<double, int>>::const_iterator' requested here
  654 |                                                                           typename E2::const_iterator::iterator_category>::iterator_category>::template
      |                                                                                        ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::vector_binary<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, double>>, const int, boost::numeric::ublas::scalar_multiplies<double, int>>, boost::numeric::ublas::scalar_plus<double, double>>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:131:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector_binary<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, double>>, const int, boost::numeric::ublas::scalar_multiplies<double, int>>, boost::numeric::ublas::scalar_plus<double, double>>>' requested here
  131 |                 vector_assign<scalar_assign> (*this, ae);
      |                 ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_proxy.hpp:139:50: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::vector<boost::numeric::ublas::vector_binary<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, double>>, const int, boost::numeric::ublas::scalar_multiplies<double, int>>, boost::numeric::ublas::scalar_plus<double, double>>>' requested here
  139 |             vector_assign<scalar_assign> (*this, typename vector_temporary_traits<M>::type (*this + ae));
      |                                                  ^
./IntRegModel.h:167:25: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>::operator+=<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, double>>, const int, boost::numeric::ublas::scalar_multiplies<double, int>>>' requested here
  167 |     ublas::row(rMat, i) += ublas::prod(csMat_, ublas::row(eMat, i)) *
      |                         ^
./TimeIndepCoxModel.h:54:32: note: in instantiation of member function 'ir::IntRegModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::initLambda' requested here
   54 |   return TimeIndepCoxPar(this->initLambda(),
      |                                ^
bayesCox.cpp:53:31: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::initPar' requested here
   53 |       TimeIndepCoxPar par(pm->initPar());
      |                               ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:653:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::vector_binary<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, double>>, const int, boost::numeric::ublas::scalar_multiplies<double, int>>, boost::numeric::ublas::scalar_plus<double, double>>::const_iterator, double>' requested here
  653 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::vector_binary<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, double>>, const int, boost::numeric::ublas::scalar_multiplies<double, int>>, boost::numeric::ublas::scalar_plus<double, double>>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:131:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector_binary<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, double>>, const int, boost::numeric::ublas::scalar_multiplies<double, int>>, boost::numeric::ublas::scalar_plus<double, double>>>' requested here
  131 |                 vector_assign<scalar_assign> (*this, ae);
      |                 ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_proxy.hpp:139:50: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::vector<boost::numeric::ublas::vector_binary<boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, double>>, const int, boost::numeric::ublas::scalar_multiplies<double, int>>, boost::numeric::ublas::scalar_plus<double, double>>>' requested here
  139 |             vector_assign<scalar_assign> (*this, typename vector_temporary_traits<M>::type (*this + ae));
      |                                                  ^
./IntRegModel.h:167:25: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>::operator+=<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_vector_prod1<boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix_row<boost::numeric::ublas::matrix<double>>, double>>, const int, boost::numeric::ublas::scalar_multiplies<double, int>>>' requested here
  167 |     ublas::row(rMat, i) += ublas::prod(csMat_, ublas::row(eMat, i)) *
      |                         ^
./TimeIndepCoxModel.h:54:32: note: in instantiation of member function 'ir::IntRegModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::initLambda' requested here
   54 |   return TimeIndepCoxPar(this->initLambda(),
      |                                ^
bayesCox.cpp:53:31: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::initPar' requested here
   53 |       TimeIndepCoxPar par(pm->initPar());
      |                               ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:4513:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::vector<int>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::vector<int>, boost::numeric::ublas::matrix<double>, double>>::const_iterator, double>' requested here
 4513 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::vector<int>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::vector<int>, boost::numeric::ublas::matrix<double>, double>>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:131:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::vector<double>, boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::vector<int>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::vector<int>, boost::numeric::ublas::matrix<double>, double>>>' requested here
  131 |                 vector_assign<scalar_assign> (*this, ae);
      |                 ^
./ublas_ext.h:101:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::vector<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::vector<int>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::vector<int>, boost::numeric::ublas::matrix<double>, double>>>' requested here
  101 |   return prod(vector<int>(m.size1(), 1), m);
      |          ^
./IntRegModel.h:171:58: note: in instantiation of function template specialization 'boost::numeric::ublas::col_sum<double>' requested here
  171 |   ublas::vector<double> lambda(ublas::element_div(ublas::col_sum(eMat),
      |                                                          ^
./TimeIndepCoxModel.h:54:32: note: in instantiation of member function 'ir::IntRegModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::initLambda' requested here
   54 |   return TimeIndepCoxPar(this->initLambda(),
      |                                ^
bayesCox.cpp:53:31: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::initPar' requested here
   53 |       TimeIndepCoxPar par(pm->initPar());
      |                               ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:653:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_divides<double, double>>::const_iterator, double>' requested here
  653 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_divides<double, double>>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:131:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_divides<double, double>>>' requested here
  131 |                 vector_assign<scalar_assign> (*this, ae);
      |                 ^
./IntRegModel.h:171:25: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::vector<boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_divides<double, double>>>' requested here
  171 |   ublas::vector<double> lambda(ublas::element_div(ublas::col_sum(eMat),
      |                         ^
./TimeIndepCoxModel.h:54:32: note: in instantiation of member function 'ir::IntRegModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>, ir::TimeIndepCoxPar>::initLambda' requested here
   54 |   return TimeIndepCoxPar(this->initLambda(),
      |                                ^
bayesCox.cpp:53:31: note: in instantiation of member function 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>::initPar' requested here
   53 |       TimeIndepCoxPar par(pm->initPar());
      |                               ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:2149:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_divides<double, double>>::const_iterator1, double>' requested here
 2149 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator1::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1364:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_divides<double, double>>::const_iterator1' requested here
 1364 |                                               typename E::const_iterator1::iterator_category,
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_divides<double, double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./GibbsSampler.h:192:25: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_divides<double, double>>>' requested here
  192 |   ublas::matrix<double> invObsLikeMat(ublas::element_div(
      |                         ^
bayesCox.cpp:54:10: note: in instantiation of member function 'ir::GibbsSampler<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>>::summaryFitR' requested here
   54 |       gs.summaryFitR(p_burn[0], p_thin[0], par,
      |          ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:2500:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_divides<double, double>>::const_iterator2, double>' requested here
 2500 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator2::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1365:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_divides<double, double>>::const_iterator2' requested here
 1365 |                                               typename E::const_iterator2::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_divides<double, double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./GibbsSampler.h:192:25: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_divides<double, double>>>' requested here
  192 |   ublas::matrix<double> invObsLikeMat(ublas::element_div(
      |                         ^
bayesCox.cpp:54:10: note: in instantiation of member function 'ir::GibbsSampler<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>>::summaryFitR' requested here
   54 |       gs.summaryFitR(p_burn[0], p_thin[0], par,
      |          ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:4513:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::vector<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::vector<double>, boost::numeric::ublas::matrix<double>, double>>::const_iterator, double>' requested here
 4513 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1333:54: note: in instantiation of member class 'boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::vector<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::vector<double>, boost::numeric::ublas::matrix<double>, double>>::const_iterator' requested here
 1333 |             public iterator_base_traits<typename E1::const_iterator::iterator_category>::template
      |                                                      ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::vector<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::vector<double>, boost::numeric::ublas::matrix<double>, double>>, const unsigned long, boost::numeric::ublas::scalar_divides<double, unsigned long>>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:131:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::vector<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::vector<double>, boost::numeric::ublas::matrix<double>, double>>, const unsigned long, boost::numeric::ublas::scalar_divides<double, unsigned long>>>' requested here
  131 |                 vector_assign<scalar_assign> (*this, ae);
      |                 ^
./ublas_ext.h:108:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::vector<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::vector<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::vector<double>, boost::numeric::ublas::matrix<double>, double>>, const unsigned long, boost::numeric::ublas::scalar_divides<double, unsigned long>>>' requested here
  108 |   return prod(vector<double>(m.size1(), 1.0), m) / m.size1();
      |          ^
./GibbsSampler.h:195:70: note: in instantiation of function template specialization 'boost::numeric::ublas::col_mean<double>' requested here
  195 |                               ublas::vector<double>(N_, 1.0), ublas::col_mean(invObsLikeMat)));
      |                                                                      ^
bayesCox.cpp:54:10: note: in instantiation of member function 'ir::GibbsSampler<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>>::summaryFitR' requested here
   54 |       gs.summaryFitR(p_burn[0], p_thin[0], par,
      |          ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1333:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::vector<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::vector<double>, boost::numeric::ublas::matrix<double>, double>>, const unsigned long, boost::numeric::ublas::scalar_divides<double, unsigned long>>::const_iterator, double>' requested here
 1333 |             public iterator_base_traits<typename E1::const_iterator::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::vector<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::vector<double>, boost::numeric::ublas::matrix<double>, double>>, const unsigned long, boost::numeric::ublas::scalar_divides<double, unsigned long>>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:131:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::vector<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::vector<double>, boost::numeric::ublas::matrix<double>, double>>, const unsigned long, boost::numeric::ublas::scalar_divides<double, unsigned long>>>' requested here
  131 |                 vector_assign<scalar_assign> (*this, ae);
      |                 ^
./ublas_ext.h:108:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::vector<boost::numeric::ublas::vector_binary_scalar2<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::vector<double>, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::vector<double>, boost::numeric::ublas::matrix<double>, double>>, const unsigned long, boost::numeric::ublas::scalar_divides<double, unsigned long>>>' requested here
  108 |   return prod(vector<double>(m.size1(), 1.0), m) / m.size1();
      |          ^
./GibbsSampler.h:195:70: note: in instantiation of function template specialization 'boost::numeric::ublas::col_mean<double>' requested here
  195 |                               ublas::vector<double>(N_, 1.0), ublas::col_mean(invObsLikeMat)));
      |                                                                      ^
bayesCox.cpp:54:10: note: in instantiation of member function 'ir::GibbsSampler<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>>::summaryFitR' requested here
   54 |       gs.summaryFitR(p_burn[0], p_thin[0], par,
      |          ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:352:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::vector_unary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_log<double>>::const_iterator, double>' requested here
  352 |             public iterator_base_traits<typename E::const_iterator::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1510:29: note: in instantiation of member class 'boost::numeric::ublas::vector_unary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_log<double>>::const_iterator' requested here
 1510 |         typedef typename E::const_iterator::iterator_category iterator_category;
      |                             ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1589:16: note: in instantiation of template class 'boost::numeric::ublas::vector_scalar_unary<boost::numeric::ublas::vector_unary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_log<double>>, boost::numeric::ublas::vector_sum<boost::numeric::ublas::vector_unary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_log<double>>>>' requested here
 1589 |         return expression_type (e ());
      |                ^
./GibbsSampler.h:198:17: note: in instantiation of function template specialization 'boost::numeric::ublas::sum<boost::numeric::ublas::vector_unary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_log<double>>>' requested here
  198 |   LPML = ublas::sum(ublas::log(CPO));
      |                 ^
bayesCox.cpp:54:10: note: in instantiation of member function 'ir::GibbsSampler<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>>::summaryFitR' requested here
   54 |       gs.summaryFitR(p_burn[0], p_thin[0], par,
      |          ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1034:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_log<double>>::const_iterator1, double>' requested here
 1034 |             public iterator_base_traits<typename E::const_iterator1::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1364:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_log<double>>::const_iterator1' requested here
 1364 |                                               typename E::const_iterator1::iterator_category,
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_log<double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./GibbsSampler.h:205:25: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_log<double>>>' requested here
  205 |   ublas::matrix<double> logObsLikeMat(ublas::log(obsLikeMat));
      |                         ^
bayesCox.cpp:54:10: note: in instantiation of member function 'ir::GibbsSampler<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>>::summaryFitR' requested here
   54 |       gs.summaryFitR(p_burn[0], p_thin[0], par,
      |          ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1205:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_log<double>>::const_iterator2, double>' requested here
 1205 |             public iterator_base_traits<typename E::const_iterator2::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1365:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_log<double>>::const_iterator2' requested here
 1365 |                                               typename E::const_iterator2::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_log<double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./GibbsSampler.h:205:25: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_log<double>>>' requested here
  205 |   ublas::matrix<double> logObsLikeMat(ublas::log(obsLikeMat));
      |                         ^
bayesCox.cpp:54:10: note: in instantiation of member function 'ir::GibbsSampler<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalPrior>>>::summaryFitR' requested here
   54 |       gs.summaryFitR(p_burn[0], p_thin[0], par,
      |          ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:17:
In file included from ./TimeIndepModel.h:15:
In file included from ./IntRegModel.h:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   44 |     delete x;
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalPrior>>>' requested here
  154 |             boost::checked_delete( p );
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:280:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalPrior>>>' requested here
  280 |     boost::detail::shared_count( p ).swap( pn );
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:374:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalPrior>>, ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalPrior>>>' requested here
  374 |         boost::detail::sp_pointer_construct( this, p, pn );
      |                        ^
bayesCox.cpp:76:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalPrior>>>::shared_ptr<ir::TimeIndepCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalPrior>>>' requested here
   76 |       boost::shared_ptr<M> pm(new M(pd));
      |                            ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1767:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>::const_iterator2, double>' requested here
 1767 |             public iterator_base_traits<typename E::const_iterator1::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:4962:19: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>::const_iterator2' requested here
 4962 |             typename E2::const_iterator2::iterator_category>::iterator_category>::template
      |                          ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1034:46: note: in instantiation of member class 'boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>::const_iterator1' requested here
 1034 |             public iterator_base_traits<typename E::const_iterator1::iterator_category>::template
      |                                                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1364:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator1' requested here
 1364 |                                               typename E::const_iterator1::iterator_category,
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./TimeVaryingCoxModel.h:65:25: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
   65 |   ublas::matrix<double> expXb(ublas::exp(ublas::prod(this->pd_->X(),
      |                         ^
./TimeVaryingCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>::gibbsKernel' requested here
   30 |   TimeVaryingCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:104:35: note: in instantiation of member function 'ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>::TimeVaryingCoxModel' requested here
  104 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:4961:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>::const_iterator1, double>' requested here
 4961 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator1::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1034:46: note: in instantiation of member class 'boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>::const_iterator1' requested here
 1034 |             public iterator_base_traits<typename E::const_iterator1::iterator_category>::template
      |                                                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1364:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator1' requested here
 1364 |                                               typename E::const_iterator1::iterator_category,
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./TimeVaryingCoxModel.h:65:25: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
   65 |   ublas::matrix<double> expXb(ublas::exp(ublas::prod(this->pd_->X(),
      |                         ^
./TimeVaryingCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>::gibbsKernel' requested here
   30 |   TimeVaryingCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:104:35: note: in instantiation of member function 'ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>::TimeVaryingCoxModel' requested here
  104 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1034:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator1, double>' requested here
 1034 |             public iterator_base_traits<typename E::const_iterator1::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1364:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator1' requested here
 1364 |                                               typename E::const_iterator1::iterator_category,
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./TimeVaryingCoxModel.h:65:25: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
   65 |   ublas::matrix<double> expXb(ublas::exp(ublas::prod(this->pd_->X(),
      |                         ^
./TimeVaryingCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>::gibbsKernel' requested here
   30 |   TimeVaryingCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:104:35: note: in instantiation of member function 'ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>::TimeVaryingCoxModel' requested here
  104 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:5223:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>::const_iterator2, double>' requested here
 5223 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator1::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1205:46: note: in instantiation of member class 'boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>::const_iterator2' requested here
 1205 |             public iterator_base_traits<typename E::const_iterator2::iterator_category>::template
      |                                                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1365:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator2' requested here
 1365 |                                               typename E::const_iterator2::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./TimeVaryingCoxModel.h:65:25: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
   65 |   ublas::matrix<double> expXb(ublas::exp(ublas::prod(this->pd_->X(),
      |                         ^
./TimeVaryingCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>::gibbsKernel' requested here
   30 |   TimeVaryingCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:104:35: note: in instantiation of member function 'ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>::TimeVaryingCoxModel' requested here
  104 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:1205:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator2, double>' requested here
 1205 |             public iterator_base_traits<typename E::const_iterator2::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1365:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>::const_iterator2' requested here
 1365 |                                               typename E::const_iterator2::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:172:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
  172 |             matrix_assign<scalar_assign> (*this, ae);
      |             ^
./TimeVaryingCoxModel.h:65:25: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::matrix<boost::numeric::ublas::matrix_unary1<boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix_unary2<boost::numeric::ublas::matrix<double>, boost::numeric::ublas::scalar_identity<double>>, double>>, boost::numeric::ublas::scalar_exp<double>>>' requested here
   65 |   ublas::matrix<double> expXb(ublas::exp(ublas::prod(this->pd_->X(),
      |                         ^
./TimeVaryingCoxModel.h:30:3: note: in instantiation of member function 'ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>::gibbsKernel' requested here
   30 |   TimeVaryingCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:104:35: note: in instantiation of member function 'ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>::TimeVaryingCoxModel' requested here
  104 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:17:
In file included from ./TimeIndepModel.h:15:
In file included from ./IntRegModel.h:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   44 |     delete x;
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>' requested here
  154 |             boost::checked_delete( p );
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:280:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>' requested here
  280 |     boost::detail::shared_count( p ).swap( pn );
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:374:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>, ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>' requested here
  374 |         boost::detail::sp_pointer_construct( this, p, pn );
      |                        ^
bayesCox.cpp:104:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>::shared_ptr<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>' requested here
  104 |       boost::shared_ptr<M> pm(new M(pd));
      |                            ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:15:
In file included from ./IntRegPrior.h:14:
In file included from /usr/local/clang18/bin/../include/c++/v1/iostream:43:
In file included from /usr/local/clang18/bin/../include/c++/v1/ios:223:
In file included from /usr/local/clang18/bin/../include/c++/v1/__locale:15:
In file included from /usr/local/clang18/bin/../include/c++/v1/__memory/shared_ptr.h:25:
/usr/local/clang18/bin/../include/c++/v1/__memory/allocator.h:176:81: warning: destructor called on non-final 'ir::TimeVaryingCoxPar' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
  176 |   _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_HIDE_FROM_ABI void destroy(pointer __p) { __p->~_Tp(); }
      |                                                                                 ^
/usr/local/clang18/bin/../include/c++/v1/__memory/allocator_traits.h:311:9: note: in instantiation of member function 'std::allocator<ir::TimeVaryingCoxPar>::destroy' requested here
  311 |     __a.destroy(__p);
      |         ^
/usr/local/clang18/bin/../include/c++/v1/vector:926:23: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<ir::TimeVaryingCoxPar>>::destroy<ir::TimeVaryingCoxPar, void>' requested here
  926 |       __alloc_traits::destroy(__alloc(), std::__to_address(--__soon_to_be_end));
      |                       ^
/usr/local/clang18/bin/../include/c++/v1/vector:920:5: note: in instantiation of member function 'std::vector<ir::TimeVaryingCoxPar>::__base_destruct_at_end' requested here
  920 |     __base_destruct_at_end(this->__begin_);
      |     ^
/usr/local/clang18/bin/../include/c++/v1/vector:490:16: note: in instantiation of member function 'std::vector<ir::TimeVaryingCoxPar>::__clear' requested here
  490 |         __vec_.__clear();
      |                ^
/usr/local/clang18/bin/../include/c++/v1/vector:501:67: note: in instantiation of member function 'std::vector<ir::TimeVaryingCoxPar>::__destroy_vector::operator()' requested here
  501 |   _LIBCPP_CONSTEXPR_SINCE_CXX20 _LIBCPP_HIDE_FROM_ABI ~vector() { __destroy_vector (*this)(); }
      |                                                                   ^
./GibbsSampler.h:40:3: note: in instantiation of member function 'std::vector<ir::TimeVaryingCoxPar>::~vector' requested here
   40 |   GibbsSampler(const boost::shared_ptr<M>& pm,
      |   ^
bayesCox.cpp:107:23: note: in instantiation of member function 'ir::GibbsSampler<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>::GibbsSampler' requested here
  107 |       GibbsSampler<M> gs(pm, p_iter[0]);
      |                       ^
/usr/local/clang18/bin/../include/c++/v1/__memory/allocator.h:176:87: note: qualify call to silence this warning
  176 |   _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_HIDE_FROM_ABI void destroy(pointer __p) { __p->~_Tp(); }
      |                                                                                       ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:17:
In file included from ./TimeIndepModel.h:15:
In file included from ./IntRegModel.h:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   44 |     delete x;
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>>' requested here
  154 |             boost::checked_delete( p );
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:280:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>>' requested here
  280 |     boost::detail::shared_count( p ).swap( pn );
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:374:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>, ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>>' requested here
  374 |         boost::detail::sp_pointer_construct( this, p, pn );
      |                        ^
bayesCox.cpp:133:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>>::shared_ptr<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>>' requested here
  133 |       boost::shared_ptr<M> pm(new M(pd));
      |                            ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:17:
In file included from ./TimeIndepModel.h:15:
In file included from ./IntRegModel.h:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   44 |     delete x;
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>>' requested here
  154 |             boost::checked_delete( p );
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:280:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>>' requested here
  280 |     boost::detail::shared_count( p ).swap( pn );
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:374:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>, ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>>' requested here
  374 |         boost::detail::sp_pointer_construct( this, p, pn );
      |                        ^
bayesCox.cpp:164:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>>::shared_ptr<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>>' requested here
  164 |       boost::shared_ptr<M> pm(new M(pd));
      |                            ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:17:
In file included from ./TimeIndepModel.h:15:
In file included from ./IntRegModel.h:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   44 |     delete x;
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>>' requested here
  154 |             boost::checked_delete( p );
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:280:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>>' requested here
  280 |     boost::detail::shared_count( p ).swap( pn );
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:374:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>, ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>>' requested here
  374 |         boost::detail::sp_pointer_construct( this, p, pn );
      |                        ^
bayesCox.cpp:193:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>>::shared_ptr<ir::TimeVaryingCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>>' requested here
  193 |       boost::shared_ptr<M> pm(new M(pd));
      |                            ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_proxy.hpp:714:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_column<boost::numeric::ublas::matrix<int>>::const_iterator, int>' requested here
  714 |             public iterator_base_traits<typename const_subiterator_type::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1510:29: note: in instantiation of member class 'boost::numeric::ublas::matrix_column<boost::numeric::ublas::matrix<int>>::const_iterator' requested here
 1510 |         typedef typename E::const_iterator::iterator_category iterator_category;
      |                             ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1589:16: note: in instantiation of template class 'boost::numeric::ublas::vector_scalar_unary<boost::numeric::ublas::matrix_column<boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::vector_sum<boost::numeric::ublas::matrix_column<boost::numeric::ublas::matrix<int>>>>' requested here
 1589 |         return expression_type (e ());
      |                ^
./DynamicCoxModel.h:93:27: note: in instantiation of function template specialization 'boost::numeric::ublas::sum<boost::numeric::ublas::matrix_column<boost::numeric::ublas::matrix<int>>>' requested here
   93 |     double nJump = ublas::sum(ublas::column(par.jump, j));
      |                           ^
./DynamicCoxModel.h:30:3: note: in instantiation of member function 'ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>::gibbsKernel' requested here
   30 |   DynamicCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:224:35: note: in instantiation of member function 'ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>::DynamicCoxModel' requested here
  224 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_proxy.hpp:265:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::vector_range<boost::numeric::ublas::vector<double>>::const_iterator, double>' requested here
  265 |             public iterator_base_traits<typename const_subiterator_type::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1510:29: note: in instantiation of member class 'boost::numeric::ublas::vector_range<boost::numeric::ublas::vector<double>>::const_iterator' requested here
 1510 |         typedef typename E::const_iterator::iterator_category iterator_category;
      |                             ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1589:16: note: in instantiation of template class 'boost::numeric::ublas::vector_scalar_unary<boost::numeric::ublas::vector_range<boost::numeric::ublas::vector<double>>, boost::numeric::ublas::vector_sum<boost::numeric::ublas::vector_range<boost::numeric::ublas::vector<double>>>>' requested here
 1589 |         return expression_type (e ());
      |                ^
./DynamicModel.h:212:26: note: in instantiation of function template specialization 'boost::numeric::ublas::sum<boost::numeric::ublas::vector_range<boost::numeric::ublas::vector<double>>>' requested here
  212 |       double wt = ublas::sum(ublas::project(this->delta_, r1)) /
      |                          ^
./DynamicCoxModel.h:101:26: note: in instantiation of member function 'ir::DynamicModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>, ir::DynamicCoxPar>::propBirth' requested here
  101 |       prop_ratio = this->propBirth(j, par.beta, par.jump, prop_par.beta,
      |                          ^
./DynamicCoxModel.h:30:3: note: in instantiation of member function 'ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>::gibbsKernel' requested here
   30 |   DynamicCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:224:35: note: in instantiation of member function 'ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>::DynamicCoxModel' requested here
  224 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_proxy.hpp:714:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_column<boost::numeric::ublas::matrix<double>>::const_iterator, double>' requested here
  714 |             public iterator_base_traits<typename const_subiterator_type::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::matrix_column<boost::numeric::ublas::matrix<double>>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:131:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::vector<double>, boost::numeric::ublas::matrix_column<boost::numeric::ublas::matrix<double>>>' requested here
  131 |                 vector_assign<scalar_assign> (*this, ae);
      |                 ^
./DynamicCoxModel.h:118:56: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::vector<boost::numeric::ublas::matrix_column<boost::numeric::ublas::matrix<double>>>' requested here
  118 |                                                        ublas::column(prop_par.beta, j),
      |                                                        ^
./DynamicCoxModel.h:30:3: note: in instantiation of member function 'ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>::gibbsKernel' requested here
   30 |   DynamicCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:224:35: note: in instantiation of member function 'ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>::DynamicCoxModel' requested here
  224 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_proxy.hpp:2975:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<int>>::const_iterator2, int>' requested here
 2975 |             public iterator_base_traits<typename const_subiterator2_type::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:4514:19: note: in instantiation of member class 'boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<int>>::const_iterator2' requested here
 4514 |             typename E2::const_iterator2::iterator_category>::iterator_category>::template
      |                          ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1510:29: note: in instantiation of member class 'boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<int>>, double>>::const_iterator' requested here
 1510 |         typedef typename E::const_iterator::iterator_category iterator_category;
      |                             ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1589:16: note: in instantiation of template class 'boost::numeric::ublas::vector_scalar_unary<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<int>>, double>>, boost::numeric::ublas::vector_sum<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<int>>, double>>>>' requested here
 1589 |         return expression_type (e ());
      |                ^
./DynamicModel.h:389:19: note: in instantiation of function template specialization 'boost::numeric::ublas::sum<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<int>>, double>>>' requested here
  389 |           (ublas::sum(ublas::prod(ublas::column(this->pd_->X(), j),
      |                   ^
./DynamicCoxModel.h:136:13: note: in instantiation of member function 'ir::DynamicModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>, ir::DynamicCoxPar>::sampleBeta' requested here
  136 |       this->sampleBeta(j, dNMat, YMat, par.lambda, par.jump, omega,
      |             ^
./DynamicCoxModel.h:30:3: note: in instantiation of member function 'ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>::gibbsKernel' requested here
   30 |   DynamicCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:224:35: note: in instantiation of member function 'ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>::DynamicCoxModel' requested here
  224 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_expression.hpp:4513:13: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<int>>, double>>::const_iterator, double>' requested here
 4513 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1510:29: note: in instantiation of member class 'boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<int>>, double>>::const_iterator' requested here
 1510 |         typedef typename E::const_iterator::iterator_category iterator_category;
      |                             ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:1589:16: note: in instantiation of template class 'boost::numeric::ublas::vector_scalar_unary<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<int>>, double>>, boost::numeric::ublas::vector_sum<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<int>>, double>>>>' requested here
 1589 |         return expression_type (e ());
      |                ^
./DynamicModel.h:389:19: note: in instantiation of function template specialization 'boost::numeric::ublas::sum<boost::numeric::ublas::matrix_vector_binary2<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<int>>, boost::numeric::ublas::matrix_vector_prod2<boost::numeric::ublas::matrix_column<const boost::numeric::ublas::matrix<double>>, boost::numeric::ublas::matrix_range<const boost::numeric::ublas::matrix<int>>, double>>>' requested here
  389 |           (ublas::sum(ublas::prod(ublas::column(this->pd_->X(), j),
      |                   ^
./DynamicCoxModel.h:136:13: note: in instantiation of member function 'ir::DynamicModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>, ir::DynamicCoxPar>::sampleBeta' requested here
  136 |       this->sampleBeta(j, dNMat, YMat, par.lambda, par.jump, omega,
      |             ^
./DynamicCoxModel.h:30:3: note: in instantiation of member function 'ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>::gibbsKernel' requested here
   30 |   DynamicCoxModel<Prior>(const boost::shared_ptr<IntRegData>& pd)
      |   ^
bayesCox.cpp:224:35: note: in instantiation of member function 'ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>::DynamicCoxModel' requested here
  224 |       boost::shared_ptr<M> pm(new M(pd));
      |                                   ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:17:
In file included from ./TimeIndepModel.h:15:
In file included from ./IntRegModel.h:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   44 |     delete x;
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>' requested here
  154 |             boost::checked_delete( p );
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:280:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>' requested here
  280 |     boost::detail::shared_count( p ).swap( pn );
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:374:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>, ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>' requested here
  374 |         boost::detail::sp_pointer_construct( this, p, pn );
      |                        ^
bayesCox.cpp:224:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>::shared_ptr<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>' requested here
  224 |       boost::shared_ptr<M> pm(new M(pd));
      |                            ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:15:
In file included from ./IntRegPrior.h:14:
In file included from /usr/local/clang18/bin/../include/c++/v1/iostream:43:
In file included from /usr/local/clang18/bin/../include/c++/v1/ios:223:
In file included from /usr/local/clang18/bin/../include/c++/v1/__locale:15:
In file included from /usr/local/clang18/bin/../include/c++/v1/__memory/shared_ptr.h:25:
/usr/local/clang18/bin/../include/c++/v1/__memory/allocator.h:176:81: warning: destructor called on non-final 'ir::DynamicCoxPar' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
  176 |   _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_HIDE_FROM_ABI void destroy(pointer __p) { __p->~_Tp(); }
      |                                                                                 ^
/usr/local/clang18/bin/../include/c++/v1/__memory/allocator_traits.h:311:9: note: in instantiation of member function 'std::allocator<ir::DynamicCoxPar>::destroy' requested here
  311 |     __a.destroy(__p);
      |         ^
/usr/local/clang18/bin/../include/c++/v1/vector:926:23: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<ir::DynamicCoxPar>>::destroy<ir::DynamicCoxPar, void>' requested here
  926 |       __alloc_traits::destroy(__alloc(), std::__to_address(--__soon_to_be_end));
      |                       ^
/usr/local/clang18/bin/../include/c++/v1/vector:920:5: note: in instantiation of member function 'std::vector<ir::DynamicCoxPar>::__base_destruct_at_end' requested here
  920 |     __base_destruct_at_end(this->__begin_);
      |     ^
/usr/local/clang18/bin/../include/c++/v1/vector:490:16: note: in instantiation of member function 'std::vector<ir::DynamicCoxPar>::__clear' requested here
  490 |         __vec_.__clear();
      |                ^
/usr/local/clang18/bin/../include/c++/v1/vector:501:67: note: in instantiation of member function 'std::vector<ir::DynamicCoxPar>::__destroy_vector::operator()' requested here
  501 |   _LIBCPP_CONSTEXPR_SINCE_CXX20 _LIBCPP_HIDE_FROM_ABI ~vector() { __destroy_vector (*this)(); }
      |                                                                   ^
./GibbsSampler.h:40:3: note: in instantiation of member function 'std::vector<ir::DynamicCoxPar>::~vector' requested here
   40 |   GibbsSampler(const boost::shared_ptr<M>& pm,
      |   ^
bayesCox.cpp:228:23: note: in instantiation of member function 'ir::GibbsSampler<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalProcessPrior>>>::GibbsSampler' requested here
  228 |       GibbsSampler<M> gs(pm, p_iter[0]);
      |                       ^
/usr/local/clang18/bin/../include/c++/v1/__memory/allocator.h:176:87: note: qualify call to silence this warning
  176 |   _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_HIDE_FROM_ABI void destroy(pointer __p) { __p->~_Tp(); }
      |                                                                                       ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:17:
In file included from ./TimeIndepModel.h:15:
In file included from ./IntRegModel.h:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   44 |     delete x;
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>>' requested here
  154 |             boost::checked_delete( p );
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:280:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>>' requested here
  280 |     boost::detail::shared_count( p ).swap( pn );
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:374:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>, ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>>' requested here
  374 |         boost::detail::sp_pointer_construct( this, p, pn );
      |                        ^
bayesCox.cpp:257:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>>::shared_ptr<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaPrior, ir::NormalInvGammaProcessPrior>>>' requested here
  257 |       boost::shared_ptr<M> pm(new M(pd));
      |                            ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:17:
In file included from ./TimeIndepModel.h:15:
In file included from ./IntRegModel.h:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalProcessPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   44 |     delete x;
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalProcessPrior>>>' requested here
  154 |             boost::checked_delete( p );
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:280:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalProcessPrior>>>' requested here
  280 |     boost::detail::shared_count( p ).swap( pn );
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:374:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalProcessPrior>>, ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalProcessPrior>>>' requested here
  374 |         boost::detail::sp_pointer_construct( this, p, pn );
      |                        ^
bayesCox.cpp:292:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalProcessPrior>>>::shared_ptr<ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalProcessPrior>>>' requested here
  292 |       boost::shared_ptr<M> pm(new M(pd));
      |                            ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:653:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_plus<double, double>>::const_iterator, double>' requested here
  653 |             public iterator_base_traits<typename iterator_restrict_traits<typename E1::const_iterator::iterator_category,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:352:53: note: in instantiation of member class 'boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_plus<double, double>>::const_iterator' requested here
  352 |             public iterator_base_traits<typename E::const_iterator::iterator_category>::template
      |                                                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::vector_unary<boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_plus<double, double>>, boost::numeric::ublas::scalar_log<double>>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:131:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector_unary<boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_plus<double, double>>, boost::numeric::ublas::scalar_log<double>>>' requested here
  131 |                 vector_assign<scalar_assign> (*this, ae);
      |                 ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_proxy.hpp:600:50: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::vector<boost::numeric::ublas::vector_unary<boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_plus<double, double>>, boost::numeric::ublas::scalar_log<double>>>' requested here
  600 |             vector_assign<scalar_assign> (*this, typename vector_temporary_traits<M>::type (ae));
      |                                                  ^
./DynamicCoxModel_v2.h:58:29: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_column<boost::numeric::ublas::matrix<double>>::operator=<boost::numeric::ublas::vector_unary<boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_plus<double, double>>, boost::numeric::ublas::scalar_log<double>>>' requested here
   58 |   ublas::column(betaMat, 0) = ublas::log(this->initLambda() +
      |                             ^
bayesCox.cpp:299:29: note: in instantiation of member function 'ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalProcessPrior>>::initPar' requested here
  299 |       DynamicCoxPar par(pm->initPar());
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:16:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector_expression.hpp:352:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::vector_unary<boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_plus<double, double>>, boost::numeric::ublas::scalar_log<double>>::const_iterator, double>' requested here
  352 |             public iterator_base_traits<typename E::const_iterator::iterator_category>::template
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::vector_unary<boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_plus<double, double>>, boost::numeric::ublas::scalar_log<double>>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:131:10: note: in instantiation of function template specialization 'boost::numeric::ublas::vector_assign<boost::numeric::ublas::scalar_assign, boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector_unary<boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_plus<double, double>>, boost::numeric::ublas::scalar_log<double>>>' requested here
  131 |                 vector_assign<scalar_assign> (*this, ae);
      |                 ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix_proxy.hpp:600:50: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::vector<boost::numeric::ublas::vector_unary<boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_plus<double, double>>, boost::numeric::ublas::scalar_log<double>>>' requested here
  600 |             vector_assign<scalar_assign> (*this, typename vector_temporary_traits<M>::type (ae));
      |                                                  ^
./DynamicCoxModel_v2.h:58:29: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_column<boost::numeric::ublas::matrix<double>>::operator=<boost::numeric::ublas::vector_unary<boost::numeric::ublas::vector_binary<boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>, boost::numeric::ublas::scalar_plus<double, double>>, boost::numeric::ublas::scalar_log<double>>>' requested here
   58 |   ublas::column(betaMat, 0) = ublas::log(this->initLambda() +
      |                             ^
bayesCox.cpp:299:29: note: in instantiation of member function 'ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalProcessPrior>>::initPar' requested here
  299 |       DynamicCoxPar par(pm->initPar());
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:17:
In file included from ./TimeIndepModel.h:15:
In file included from ./IntRegModel.h:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalInvGammaProcessPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   44 |     delete x;
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalInvGammaProcessPrior>>>' requested here
  154 |             boost::checked_delete( p );
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:280:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalInvGammaProcessPrior>>>' requested here
  280 |     boost::detail::shared_count( p ).swap( pn );
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:374:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalInvGammaProcessPrior>>, ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalInvGammaProcessPrior>>>' requested here
  374 |         boost::detail::sp_pointer_construct( this, p, pn );
      |                        ^
bayesCox.cpp:324:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalInvGammaProcessPrior>>>::shared_ptr<ir::DynamicCoxModel_v2<ir::CoxPrior<ir::ConstValuePrior, ir::NormalInvGammaProcessPrior>>>' requested here
  324 |       boost::shared_ptr<M> pm(new M(pd));
      |                            ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:17:
In file included from ./TimeIndepModel.h:15:
In file included from ./IntRegModel.h:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   44 |     delete x;
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>>' requested here
  154 |             boost::checked_delete( p );
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:280:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>>' requested here
  280 |     boost::detail::shared_count( p ).swap( pn );
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:374:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>, ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>>' requested here
  374 |         boost::detail::sp_pointer_construct( this, p, pn );
      |                        ^
bayesCox.cpp:359:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>>::shared_ptr<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalProcessPrior>>>' requested here
  359 |       boost::shared_ptr<M> pm(new M(pd));
      |                            ^
In file included from bayesCox.cpp:3:
In file included from ./TimeIndepCoxModel.h:17:
In file included from ./TimeIndepModel.h:15:
In file included from ./IntRegModel.h:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/data/gannet/ripley/R/test-clang/BH/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
   44 |     delete x;
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>>' requested here
  154 |             boost::checked_delete( p );
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:280:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>>' requested here
  280 |     boost::detail::shared_count( p ).swap( pn );
      |     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/shared_ptr.hpp:374:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>, ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>>' requested here
  374 |         boost::detail::sp_pointer_construct( this, p, pn );
      |                        ^
bayesCox.cpp:392:28: note: in instantiation of function template specialization 'boost::shared_ptr<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>>::shared_ptr<ir::DynamicCoxModel<ir::CoxPrior<ir::GammaProcessPrior, ir::NormalInvGammaProcessPrior>>>' requested here
  392 |       boost::shared_ptr<M> pm(new M(pd));
      |                            ^
In file included from IntRegPar.cpp:10:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:518:18: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::vector<double>::const_iterator, double>' requested here
  518 |                  public random_access_iterator_base<dense_random_access_iterator_tag,
      |                         ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/vector_assign.hpp:486:59: note: in instantiation of member class 'boost::numeric::ublas::vector<double>::const_iterator' requested here
  486 |                                               typename E::const_iterator::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:385:11: note: in instantiation of function template specialization 'boost::numeric::ublas::vector_assign<boost::numeric::ublas::scalar_plus_assign, boost::numeric::ublas::vector<double>, boost::numeric::ublas::vector<double>>' requested here
  385 |                  vector_assign<scalar_plus_assign> (*this, ae);
      |                  ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:372:11: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::plus_assign<boost::numeric::ublas::vector<double>>' requested here
  372 |                  plus_assign (v);
      |                  ^
./IntRegPar.h:147:16: note: in instantiation of function template specialization 'boost::numeric::ublas::vector<double>::operator+=<boost::numeric::ublas::vector<double>>' requested here
  147 |     par.lambda += vp[i].lambda;
      |                ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from IntRegPar.cpp:10:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:486:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix<double>::const_iterator1, double>' requested here
  486 |             public random_access_iterator_base<dense_random_access_iterator_tag,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1364:59: note: in instantiation of member class 'boost::numeric::ublas::matrix<double>::const_iterator1' requested here
 1364 |                                               typename E::const_iterator1::iterator_category,
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:377:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_plus_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>>' requested here
  377 |             matrix_assign<scalar_plus_assign> (*this, ae);
      |             ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:371:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::plus_assign<boost::numeric::ublas::matrix<double>>' requested here
  371 |             plus_assign (m);
      |             ^
./IntRegPar.h:195:14: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::operator+=<boost::numeric::ublas::matrix<double>>' requested here
  195 |     par.beta += vp[i].beta;
      |              ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from IntRegPar.cpp:10:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:809:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix<double>::const_iterator2, double>' requested here
  809 |             public random_access_iterator_base<dense_random_access_iterator_tag,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1365:59: note: in instantiation of member class 'boost::numeric::ublas::matrix<double>::const_iterator2' requested here
 1365 |                                               typename E::const_iterator2::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:377:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_plus_assign, boost::numeric::ublas::matrix<double>, boost::numeric::ublas::matrix<double>>' requested here
  377 |             matrix_assign<scalar_plus_assign> (*this, ae);
      |             ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:371:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::plus_assign<boost::numeric::ublas::matrix<double>>' requested here
  371 |             plus_assign (m);
      |             ^
./IntRegPar.h:195:14: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<double>::operator+=<boost::numeric::ublas::matrix<double>>' requested here
  195 |     par.beta += vp[i].beta;
      |              ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, double>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from IntRegPar.cpp:10:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:486:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix<int>::const_iterator1, int>' requested here
  486 |             public random_access_iterator_base<dense_random_access_iterator_tag,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1364:59: note: in instantiation of member class 'boost::numeric::ublas::matrix<int>::const_iterator1' requested here
 1364 |                                               typename E::const_iterator1::iterator_category,
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:377:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_plus_assign, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix<int>>' requested here
  377 |             matrix_assign<scalar_plus_assign> (*this, ae);
      |             ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:371:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<int>::plus_assign<boost::numeric::ublas::matrix<int>>' requested here
  371 |             plus_assign (m);
      |             ^
./IntRegPar.h:235:14: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<int>::operator+=<boost::numeric::ublas::matrix<int>>' requested here
  235 |     par.jump += vp[i].jump;
      |              ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
In file included from IntRegPar.cpp:10:
In file included from ./IntRegPar.h:15:
In file included from ./ublas.h:14:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/vector.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/storage.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/traits.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/iterator.hpp:204:21: warning: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' is deprecated [-Wdeprecated-declarations]
  204 |         public std::iterator<IC, T> {
      |                     ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:809:20: note: in instantiation of template class 'boost::numeric::ublas::random_access_iterator_base<boost::numeric::ublas::dense_random_access_iterator_tag, boost::numeric::ublas::matrix<int>::const_iterator2, int>' requested here
  809 |             public random_access_iterator_base<dense_random_access_iterator_tag,
      |                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/detail/matrix_assign.hpp:1365:59: note: in instantiation of member class 'boost::numeric::ublas::matrix<int>::const_iterator2' requested here
 1365 |                                               typename E::const_iterator2::iterator_category>::storage_category storage_category;
      |                                                           ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:377:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_plus_assign, boost::numeric::ublas::matrix<int>, boost::numeric::ublas::matrix<int>>' requested here
  377 |             matrix_assign<scalar_plus_assign> (*this, ae);
      |             ^
/data/gannet/ripley/R/test-clang/BH/include/boost/numeric/ublas/matrix.hpp:371:13: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<int>::plus_assign<boost::numeric::ublas::matrix<int>>' requested here
  371 |             plus_assign (m);
      |             ^
./IntRegPar.h:235:14: note: in instantiation of function template specialization 'boost::numeric::ublas::matrix<int>::operator+=<boost::numeric::ublas::matrix<int>>' requested here
  235 |     par.jump += vp[i].jump;
      |              ^
/usr/local/clang18/bin/../include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<boost::numeric::ublas::dense_random_access_iterator_tag, int>' has been explicitly marked deprecated here
   23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
      |                             ^
/usr/local/clang18/bin/../include/c++/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
 1001 | #    define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
      |                                         ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
  974 | #      define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
      |                                                 ^
6 warnings generated.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DNDEBUG -DBOOST_NO_AUTO_PTR -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c dynsurv_init.c -o dynsurv_init.o
78 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o dynsurv.so IntRegPar.o arms.o bayesCox.o dynsurv_init.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/dynsurv/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/dynsurv/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/dynsurv/src'
installing to /data/gannet/ripley/R/packages/tests-clang/dynsurv.Rcheck/00LOCK-dynsurv/00new/dynsurv/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (dynsurv)