* installing *source* package ‘hmmTMB’ ...
** this is package ‘hmmTMB’ version ‘1.1.0’
** 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 21.1.0-rc3’
make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/hmmTMB/src'
/usr/local/clang21/bin/clang++ -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/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -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: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));
| ^
/data/gannet/ripley/R/test-clang/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 /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/clang21/bin/../include/c++/v1/iostream:45:
In file included from /usr/local/clang21/bin/../include/c++/v1/ios:228:
In file included from /usr/local/clang21/bin/../include/c++/v1/__locale:28:
In file included from /usr/local/clang21/bin/../include/c++/v1/string:654:
In file included from /usr/local/clang21/bin/../include/c++/v1/string_view:951:
In file included from /usr/local/clang21/bin/../include/c++/v1/algorithm:1865:
In file included from /usr/local/clang21/bin/../include/c++/v1/__algorithm/inplace_merge.h:27:
/usr/local/clang21/bin/../include/c++/v1/__memory/unique_ptr.h:77:5: warning: delete called on 'Dist<CppAD::AD<double>>' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
77 | delete __ptr;
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/unique_ptr.h:290:7: note: in instantiation of member function 'std::default_delete<Dist<CppAD::AD<double>>>::operator()' requested here
290 | __deleter_(__tmp);
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/unique_ptr.h:259:71: note: in instantiation of member function 'std::unique_ptr<Dist<CppAD::AD<double>>>::reset' requested here
259 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX23 ~unique_ptr() { reset(); }
| ^
./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));
| ^
/data/gannet/ripley/R/test-clang/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));
| ^
/data/gannet/ripley/R/test-clang/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()() ) );
| ^
/data/gannet/ripley/R/R-clang/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT'
388 | #define PROTECT(s) Rf_protect(s)
| ^
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/clang21/bin/../include/c++/v1/iostream:45:
In file included from /usr/local/clang21/bin/../include/c++/v1/ios:228:
In file included from /usr/local/clang21/bin/../include/c++/v1/__locale:28:
In file included from /usr/local/clang21/bin/../include/c++/v1/string:654:
In file included from /usr/local/clang21/bin/../include/c++/v1/string_view:951:
In file included from /usr/local/clang21/bin/../include/c++/v1/algorithm:1865:
In file included from /usr/local/clang21/bin/../include/c++/v1/__algorithm/inplace_merge.h:27:
/usr/local/clang21/bin/../include/c++/v1/__memory/unique_ptr.h:77:5: warning: delete called on 'Dist<double>' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
77 | delete __ptr;
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/unique_ptr.h:290:7: note: in instantiation of member function 'std::default_delete<Dist<double>>::operator()' requested here
290 | __deleter_(__tmp);
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/unique_ptr.h:259:71: note: in instantiation of member function 'std::unique_ptr<Dist<double>>::reset' requested here
259 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX23 ~unique_ptr() { reset(); }
| ^
./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));
| ^
/data/gannet/ripley/R/test-clang/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()() ) );
| ^
/data/gannet/ripley/R/R-clang/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT'
388 | #define PROTECT(s) Rf_protect(s)
| ^
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));
| ^
/data/gannet/ripley/R/test-clang/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()();
| ^
/data/gannet/ripley/R/test-clang/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 /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/clang21/bin/../include/c++/v1/iostream:45:
In file included from /usr/local/clang21/bin/../include/c++/v1/ios:228:
In file included from /usr/local/clang21/bin/../include/c++/v1/__locale:28:
In file included from /usr/local/clang21/bin/../include/c++/v1/string:654:
In file included from /usr/local/clang21/bin/../include/c++/v1/string_view:951:
In file included from /usr/local/clang21/bin/../include/c++/v1/algorithm:1865:
In file included from /usr/local/clang21/bin/../include/c++/v1/__algorithm/inplace_merge.h:27:
/usr/local/clang21/bin/../include/c++/v1/__memory/unique_ptr.h:77:5: warning: delete called on 'Dist<CppAD::AD<CppAD::AD<double>>>' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
77 | delete __ptr;
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/unique_ptr.h:290:7: note: in instantiation of member function 'std::default_delete<Dist<CppAD::AD<CppAD::AD<double>>>>::operator()' requested here
290 | __deleter_(__tmp);
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/unique_ptr.h:259:71: note: in instantiation of member function 'std::unique_ptr<Dist<CppAD::AD<CppAD::AD<double>>>>::reset' requested here
259 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX23 ~unique_ptr() { reset(); }
| ^
./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));
| ^
/data/gannet/ripley/R/test-clang/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()();
| ^
/data/gannet/ripley/R/test-clang/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));
| ^
/data/gannet/ripley/R/test-clang/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()();
| ^
/data/gannet/ripley/R/test-clang/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 /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/clang21/bin/../include/c++/v1/iostream:45:
In file included from /usr/local/clang21/bin/../include/c++/v1/ios:228:
In file included from /usr/local/clang21/bin/../include/c++/v1/__locale:28:
In file included from /usr/local/clang21/bin/../include/c++/v1/string:654:
In file included from /usr/local/clang21/bin/../include/c++/v1/string_view:951:
In file included from /usr/local/clang21/bin/../include/c++/v1/algorithm:1865:
In file included from /usr/local/clang21/bin/../include/c++/v1/__algorithm/inplace_merge.h:27:
/usr/local/clang21/bin/../include/c++/v1/__memory/unique_ptr.h:77:5: 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]
77 | delete __ptr;
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/unique_ptr.h:290:7: note: in instantiation of member function 'std::default_delete<Dist<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>>::operator()' requested here
290 | __deleter_(__tmp);
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/unique_ptr.h:259:71: note: in instantiation of member function 'std::unique_ptr<Dist<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>>::reset' requested here
259 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX23 ~unique_ptr() { reset(); }
| ^
./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));
| ^
/data/gannet/ripley/R/test-clang/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()();
| ^
/data/gannet/ripley/R/test-clang/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.
/usr/local/clang21/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -L/usr/local/clang21/lib/clang/21/lib/x86_64-unknown-linux-gnu -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)