* installing *source* package ‘hmmTMB’ ...
** package ‘hmmTMB’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/hmmTMB/src'
/data/gannet/ripley/R/R-clang/bin/Rscript --vanilla -e "invisible(TMB::compile('hmmTMB.cpp', safebounds = FALSE, safeunload = FALSE))"
using C++ compiler: ‘clang version 19.1.5’
make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/hmmTMB/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"/data/gannet/ripley/R/test-clang/TMB/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_hmmTMB -DCPPAD_FRAMEWORK -I'/data/gannet/ripley/R/test-clang/TMB/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c hmmTMB.cpp -o hmmTMB.o
In file included from hmmTMB.cpp:2:
In file included from ./hmmTMB.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:96:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/gannet/ripley/R/test-clang/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 /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:96:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/gannet/ripley/R/test-clang/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
| ^
/data/gannet/ripley/R/test-clang/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:4:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:46:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/Rstream.hpp:10:
In file included from /usr/local/clang19/bin/../include/c++/v1/iostream:42:
In file included from /usr/local/clang19/bin/../include/c++/v1/ios:220:
In file included from /usr/local/clang19/bin/../include/c++/v1/__locale:15:
In file included from /usr/local/clang19/bin/../include/c++/v1/__memory/shared_ptr.h:32:
/usr/local/clang19/bin/../include/c++/v1/__memory/unique_ptr.h:80:5: warning: delete called on 'Dist<CppAD::AD<double>>' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
80 | delete __ptr;
| ^
/usr/local/clang19/bin/../include/c++/v1/__memory/unique_ptr.h:292:7: note: in instantiation of member function 'std::default_delete<Dist<CppAD::AD<double>>>::operator()' requested here
292 | __ptr_.second()(__tmp);
| ^
/usr/local/clang19/bin/../include/c++/v1/__memory/unique_ptr.h:261:71: note: in instantiation of member function 'std::unique_ptr<Dist<CppAD::AD<double>>>::reset' requested here
261 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX23 ~unique_ptr() { reset(); }
| ^
./hmmTMB.hpp:154:43: note: in instantiation of member function 'std::unique_ptr<Dist<CppAD::AD<double>>>::~unique_ptr' requested here
154 | std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
| ^
/data/gannet/ripley/R/test-clang/TMB/include/tmb_core.hpp:1308:6: note: in instantiation of member function 'objective_function<CppAD::AD<double>>::operator()' requested here
1308 | 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 /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:46:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/Rstream.hpp:10:
In file included from /usr/local/clang19/bin/../include/c++/v1/iostream:42:
In file included from /usr/local/clang19/bin/../include/c++/v1/ios:220:
In file included from /usr/local/clang19/bin/../include/c++/v1/__locale:15:
In file included from /usr/local/clang19/bin/../include/c++/v1/__memory/shared_ptr.h:32:
/usr/local/clang19/bin/../include/c++/v1/__memory/unique_ptr.h:80:5: warning: delete called on 'Dist<double>' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
80 | delete __ptr;
| ^
/usr/local/clang19/bin/../include/c++/v1/__memory/unique_ptr.h:292:7: note: in instantiation of member function 'std::default_delete<Dist<double>>::operator()' requested here
292 | __ptr_.second()(__tmp);
| ^
/usr/local/clang19/bin/../include/c++/v1/__memory/unique_ptr.h:261:71: note: in instantiation of member function 'std::unique_ptr<Dist<double>>::reset' requested here
261 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX23 ~unique_ptr() { reset(); }
| ^
./hmmTMB.hpp:154:43: note: in instantiation of member function 'std::unique_ptr<Dist<double>>::~unique_ptr' requested here
154 | std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
| ^
/data/gannet/ripley/R/test-clang/TMB/include/tmb_core.hpp:2031:34: note: in instantiation of member function 'objective_function<double>::operator()' requested here
2031 | PROTECT( res = asSEXP( pf->operator()() ) );
| ^
In file included from hmmTMB.cpp:2:
In file included from ./hmmTMB.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:46:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/Rstream.hpp:10:
In file included from /usr/local/clang19/bin/../include/c++/v1/iostream:42:
In file included from /usr/local/clang19/bin/../include/c++/v1/ios:220:
In file included from /usr/local/clang19/bin/../include/c++/v1/__locale:15:
In file included from /usr/local/clang19/bin/../include/c++/v1/__memory/shared_ptr.h:32:
/usr/local/clang19/bin/../include/c++/v1/__memory/unique_ptr.h:80:5: warning: delete called on 'Dist<CppAD::AD<CppAD::AD<double>>>' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
80 | delete __ptr;
| ^
/usr/local/clang19/bin/../include/c++/v1/__memory/unique_ptr.h:292:7: note: in instantiation of member function 'std::default_delete<Dist<CppAD::AD<CppAD::AD<double>>>>::operator()' requested here
292 | __ptr_.second()(__tmp);
| ^
/usr/local/clang19/bin/../include/c++/v1/__memory/unique_ptr.h:261:71: note: in instantiation of member function 'std::unique_ptr<Dist<CppAD::AD<CppAD::AD<double>>>>::reset' requested here
261 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX23 ~unique_ptr() { reset(); }
| ^
./hmmTMB.hpp:154:43: note: in instantiation of member function 'std::unique_ptr<Dist<CppAD::AD<CppAD::AD<double>>>>::~unique_ptr' requested here
154 | std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
| ^
/data/gannet/ripley/R/test-clang/TMB/include/tmb_core.hpp:913:20: note: in instantiation of member function 'objective_function<CppAD::AD<CppAD::AD<double>>>::operator()' requested here
913 | Type ans=this->operator()();
| ^
/data/gannet/ripley/R/test-clang/TMB/include/tmb_core.hpp:2112:10: note: in instantiation of member function 'objective_function<CppAD::AD<CppAD::AD<double>>>::evalUserTemplate' requested here
2112 | y[0]=F.evalUserTemplate();
| ^
In file included from hmmTMB.cpp:2:
In file included from ./hmmTMB.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:46:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/Rstream.hpp:10:
In file included from /usr/local/clang19/bin/../include/c++/v1/iostream:42:
In file included from /usr/local/clang19/bin/../include/c++/v1/ios:220:
In file included from /usr/local/clang19/bin/../include/c++/v1/__locale:15:
In file included from /usr/local/clang19/bin/../include/c++/v1/__memory/shared_ptr.h:32:
/usr/local/clang19/bin/../include/c++/v1/__memory/unique_ptr.h:80:5: 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]
80 | delete __ptr;
| ^
/usr/local/clang19/bin/../include/c++/v1/__memory/unique_ptr.h:292:7: note: in instantiation of member function 'std::default_delete<Dist<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>>::operator()' requested here
292 | __ptr_.second()(__tmp);
| ^
/usr/local/clang19/bin/../include/c++/v1/__memory/unique_ptr.h:261:71: note: in instantiation of member function 'std::unique_ptr<Dist<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>>::reset' requested here
261 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX23 ~unique_ptr() { reset(); }
| ^
./hmmTMB.hpp:154:43: note: in instantiation of member function 'std::unique_ptr<Dist<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>>::~unique_ptr' requested here
154 | std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
| ^
/data/gannet/ripley/R/test-clang/TMB/include/tmb_core.hpp:913:20: note: in instantiation of member function 'objective_function<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>::operator()' requested here
913 | Type ans=this->operator()();
| ^
/data/gannet/ripley/R/test-clang/TMB/include/tmb_core.hpp:2361:12: note: in instantiation of member function 'objective_function<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>::evalUserTemplate' requested here
2361 | y[0] = F.evalUserTemplate();
| ^
7 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o hmmTMB.so hmmTMB.o
make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/hmmTMB/src'
make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/hmmTMB/src'
make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/hmmTMB/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/hmmTMB/src'
installing to /data/gannet/ripley/R/packages/tests-clang/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)