* installing *source* package ‘hmmTMB’ ...
** this is package ‘hmmTMB’ version ‘1.1.0’
** using staged installation
** libs
/home/hornik/tmp/R/bin/Rscript --vanilla -e "invisible(TMB::compile('hmmTMB.cpp', safebounds = FALSE, safeunload = FALSE))"
Note: Using Makevars in /home/hornik/.R/Makevars-clang 
using C++ compiler: ‘Debian clang version 19.1.7 (3+b1)’
make[1]: Entering directory '/srv/hornik/tmp/CRAN_pretest/hmmTMB.Rcheck/00_pkg_src/hmmTMB/src'
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I"/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include" -I"/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_hmmTMB  -DCPPAD_FRAMEWORK -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator  -c hmmTMB.cpp -o hmmTMB.o
In file included from hmmTMB.cpp:2:
In file included from ./hmmTMB.hpp:4:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/TMB.hpp:96:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:26:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseCore:61:
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from hmmTMB.cpp:2:
In file included from ./hmmTMB.hpp:4:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/TMB.hpp:96:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:29:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseLU:35:
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
   78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
      |         ^
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
   79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
      |         ^
In file included from hmmTMB.cpp:2:
In file included from ./hmmTMB.hpp:9:
In file included from ./dist.hpp:7:
./dist_def.hpp:980:28: warning: variables 'i' and 'dim' used in loop condition not modified in loop body [-Wfor-loop-analysis]
  980 |         for(int i = j + 1; i < dim; j++) {
      |                            ^   ~~~
./dist_def.hpp:940:3: note: in instantiation of member function 'MultivariateNormal<CppAD::AD<double>>::link' requested here
  940 |   MultivariateNormal() {}; 
      |   ^
./dist.hpp:34:44: note: in instantiation of member function 'MultivariateNormal<CppAD::AD<double>>::MultivariateNormal' requested here
   34 |     return(std::unique_ptr<Dist<Type>>(new MultivariateNormal<Type>)); 
      |                                            ^
./hmmTMB.hpp:165:44: note: in instantiation of function template specialization 'dist_generator<CppAD::AD<double>>' requested here
  165 |      std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
      |                                            ^
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/tmb_core.hpp:1312:6: note: in instantiation of member function 'objective_function<CppAD::AD<double>>::operator()' requested here
 1312 |     F(); // Run through user template (modifies reportvector)
      |      ^
In file included from hmmTMB.cpp:2:
In file included from ./hmmTMB.hpp:4:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/TMB.hpp:125:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/cppad/cppad.hpp:22:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/cppad/base_require.hpp:161:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/cppad/local/base_complex.hpp:19:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/cppad/thread_alloc.hpp:18:
In file included from /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/memory:78:
/usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/unique_ptr.h:93:2: warning: delete called on 'Dist<CppAD::AD<double>>' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
   93 |         delete __ptr;
      |         ^
/usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/unique_ptr.h:399:4: note: in instantiation of member function 'std::default_delete<Dist<CppAD::AD<double>>>::operator()' requested here
  399 |           get_deleter()(std::move(__ptr));
      |           ^
./hmmTMB.hpp:165:44: note: in instantiation of member function 'std::unique_ptr<Dist<CppAD::AD<double>>>::~unique_ptr' requested here
  165 |      std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
      |                                            ^
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/tmb_core.hpp:1312:6: note: in instantiation of member function 'objective_function<CppAD::AD<double>>::operator()' requested here
 1312 |     F(); // Run through user template (modifies reportvector)
      |      ^
In file included from hmmTMB.cpp:2:
In file included from ./hmmTMB.hpp:9:
In file included from ./dist.hpp:7:
./dist_def.hpp:980:28: warning: variables 'i' and 'dim' used in loop condition not modified in loop body [-Wfor-loop-analysis]
  980 |         for(int i = j + 1; i < dim; j++) {
      |                            ^   ~~~
./dist_def.hpp:940:3: note: in instantiation of member function 'MultivariateNormal<double>::link' requested here
  940 |   MultivariateNormal() {}; 
      |   ^
./dist.hpp:34:44: note: in instantiation of member function 'MultivariateNormal<double>::MultivariateNormal' requested here
   34 |     return(std::unique_ptr<Dist<Type>>(new MultivariateNormal<Type>)); 
      |                                            ^
./hmmTMB.hpp:165:44: note: in instantiation of function template specialization 'dist_generator<double>' requested here
  165 |      std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
      |                                            ^
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/tmb_core.hpp:2035:34: note: in instantiation of member function 'objective_function<double>::operator()' requested here
 2035 |       PROTECT( res = asSEXP( pf->operator()() ) );
      |                                  ^
In file included from hmmTMB.cpp:2:
In file included from ./hmmTMB.hpp:4:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/TMB.hpp:125:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/cppad/cppad.hpp:22:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/cppad/base_require.hpp:161:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/cppad/local/base_complex.hpp:19:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/cppad/thread_alloc.hpp:18:
In file included from /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/memory:78:
/usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/unique_ptr.h:93:2: warning: delete called on 'Dist<double>' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
   93 |         delete __ptr;
      |         ^
/usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/unique_ptr.h:399:4: note: in instantiation of member function 'std::default_delete<Dist<double>>::operator()' requested here
  399 |           get_deleter()(std::move(__ptr));
      |           ^
./hmmTMB.hpp:165:44: note: in instantiation of member function 'std::unique_ptr<Dist<double>>::~unique_ptr' requested here
  165 |      std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
      |                                            ^
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/tmb_core.hpp:2035:34: note: in instantiation of member function 'objective_function<double>::operator()' requested here
 2035 |       PROTECT( res = asSEXP( pf->operator()() ) );
      |                                  ^
In file included from hmmTMB.cpp:2:
In file included from ./hmmTMB.hpp:9:
In file included from ./dist.hpp:7:
./dist_def.hpp:980:28: warning: variables 'i' and 'dim' used in loop condition not modified in loop body [-Wfor-loop-analysis]
  980 |         for(int i = j + 1; i < dim; j++) {
      |                            ^   ~~~
./dist_def.hpp:940:3: note: in instantiation of member function 'MultivariateNormal<CppAD::AD<CppAD::AD<double>>>::link' requested here
  940 |   MultivariateNormal() {}; 
      |   ^
./dist.hpp:34:44: note: in instantiation of member function 'MultivariateNormal<CppAD::AD<CppAD::AD<double>>>::MultivariateNormal' requested here
   34 |     return(std::unique_ptr<Dist<Type>>(new MultivariateNormal<Type>)); 
      |                                            ^
./hmmTMB.hpp:165:44: note: in instantiation of function template specialization 'dist_generator<CppAD::AD<CppAD::AD<double>>>' requested here
  165 |      std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
      |                                            ^
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/tmb_core.hpp:917:20: note: in instantiation of member function 'objective_function<CppAD::AD<CppAD::AD<double>>>::operator()' requested here
  917 |     Type ans=this->operator()();
      |                    ^
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/tmb_core.hpp:2116:10: note: in instantiation of member function 'objective_function<CppAD::AD<CppAD::AD<double>>>::evalUserTemplate' requested here
 2116 |   y[0]=F.evalUserTemplate();
      |          ^
In file included from hmmTMB.cpp:2:
In file included from ./hmmTMB.hpp:4:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/TMB.hpp:125:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/cppad/cppad.hpp:22:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/cppad/base_require.hpp:161:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/cppad/local/base_complex.hpp:19:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/cppad/thread_alloc.hpp:18:
In file included from /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/memory:78:
/usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/unique_ptr.h:93:2: warning: delete called on 'Dist<CppAD::AD<CppAD::AD<double>>>' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
   93 |         delete __ptr;
      |         ^
/usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/unique_ptr.h:399:4: note: in instantiation of member function 'std::default_delete<Dist<CppAD::AD<CppAD::AD<double>>>>::operator()' requested here
  399 |           get_deleter()(std::move(__ptr));
      |           ^
./hmmTMB.hpp:165:44: note: in instantiation of member function 'std::unique_ptr<Dist<CppAD::AD<CppAD::AD<double>>>>::~unique_ptr' requested here
  165 |      std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
      |                                            ^
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/tmb_core.hpp:917:20: note: in instantiation of member function 'objective_function<CppAD::AD<CppAD::AD<double>>>::operator()' requested here
  917 |     Type ans=this->operator()();
      |                    ^
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/tmb_core.hpp:2116:10: note: in instantiation of member function 'objective_function<CppAD::AD<CppAD::AD<double>>>::evalUserTemplate' requested here
 2116 |   y[0]=F.evalUserTemplate();
      |          ^
In file included from hmmTMB.cpp:2:
In file included from ./hmmTMB.hpp:9:
In file included from ./dist.hpp:7:
./dist_def.hpp:980:28: warning: variables 'i' and 'dim' used in loop condition not modified in loop body [-Wfor-loop-analysis]
  980 |         for(int i = j + 1; i < dim; j++) {
      |                            ^   ~~~
./dist_def.hpp:940:3: note: in instantiation of member function 'MultivariateNormal<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>::link' requested here
  940 |   MultivariateNormal() {}; 
      |   ^
./dist.hpp:34:44: note: in instantiation of member function 'MultivariateNormal<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>::MultivariateNormal' requested here
   34 |     return(std::unique_ptr<Dist<Type>>(new MultivariateNormal<Type>)); 
      |                                            ^
./hmmTMB.hpp:165:44: note: in instantiation of function template specialization 'dist_generator<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>' requested here
  165 |      std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
      |                                            ^
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/tmb_core.hpp:917:20: note: in instantiation of member function 'objective_function<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>::operator()' requested here
  917 |     Type ans=this->operator()();
      |                    ^
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/tmb_core.hpp:2365:12: note: in instantiation of member function 'objective_function<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>::evalUserTemplate' requested here
 2365 |   y[0] = F.evalUserTemplate();
      |            ^
In file included from hmmTMB.cpp:2:
In file included from ./hmmTMB.hpp:4:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/TMB.hpp:125:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/cppad/cppad.hpp:22:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/cppad/base_require.hpp:161:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/cppad/local/base_complex.hpp:19:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/cppad/thread_alloc.hpp:18:
In file included from /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/memory:78:
/usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/unique_ptr.h:93:2: warning: delete called on 'Dist<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
   93 |         delete __ptr;
      |         ^
/usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/unique_ptr.h:399:4: note: in instantiation of member function 'std::default_delete<Dist<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>>::operator()' requested here
  399 |           get_deleter()(std::move(__ptr));
      |           ^
./hmmTMB.hpp:165:44: note: in instantiation of member function 'std::unique_ptr<Dist<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>>::~unique_ptr' requested here
  165 |      std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
      |                                            ^
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/tmb_core.hpp:917:20: note: in instantiation of member function 'objective_function<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>::operator()' requested here
  917 |     Type ans=this->operator()();
      |                    ^
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include/tmb_core.hpp:2365:12: note: in instantiation of member function 'objective_function<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>::evalUserTemplate' requested here
 2365 |   y[0] = F.evalUserTemplate();
      |            ^
11 warnings generated.
clang++-19 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o hmmTMB.so hmmTMB.o -L/home/hornik/tmp/R/lib -lR
make[1]: Leaving directory '/srv/hornik/tmp/CRAN_pretest/hmmTMB.Rcheck/00_pkg_src/hmmTMB/src'
make[1]: Entering directory '/srv/hornik/tmp/CRAN_pretest/hmmTMB.Rcheck/00_pkg_src/hmmTMB/src'
make[1]: Leaving directory '/srv/hornik/tmp/CRAN_pretest/hmmTMB.Rcheck/00_pkg_src/hmmTMB/src'
installing to /srv/hornik/tmp/CRAN_pretest/hmmTMB.Rcheck/00LOCK-hmmTMB/00new/hmmTMB/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (hmmTMB)