* installing *source* package ‘hmmTMB’ ...
** this is package ‘hmmTMB’ version ‘1.1.2’
** package ‘hmmTMB’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
/Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "invisible(TMB::compile('hmmTMB.cpp', safebounds = FALSE, safeunload = FALSE))"
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.3.19.1)’
using SDK: ‘MacOSX14.5.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/TMB/include" -I"/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_hmmTMB -DCPPAD_FRAMEWORK -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/TMB/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmmTMB.cpp -o hmmTMB.o
In file included from hmmTMB.cpp:2:
In file included from ./hmmTMB.hpp:4:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/TMB/include/TMB.hpp:96:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:26:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseCore:61:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/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 /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/TMB/include/TMB.hpp:96:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:29:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseLU:35:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/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
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/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:1040:28: warning: variables 'i' and 'dim' used in loop condition not modified in loop body [-Wfor-loop-analysis]
1040 | for(int i = j + 1; i < dim; j++) {
| ^ ~~~
./dist_def.hpp:1000:3: note: in instantiation of member function 'MultivariateNormal<CppAD::AD<double>>::link' requested here
1000 | MultivariateNormal() {};
| ^
./dist.hpp:36:44: note: in instantiation of member function 'MultivariateNormal<CppAD::AD<double>>::MultivariateNormal' requested here
36 | 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));
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/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 /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/TMB/include/TMB.hpp:46:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/TMB/include/Rstream.hpp:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/ios:222:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__locale:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__memory/shared_ptr.h:31:
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__memory/unique_ptr.h:68:5: warning: delete called on 'Dist<CppAD::AD<double>>' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
68 | delete __ptr;
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__memory/unique_ptr.h:300:7: note: in instantiation of member function 'std::default_delete<Dist<CppAD::AD<double>>>::operator()' requested here
300 | __ptr_.second()(__tmp);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__memory/unique_ptr.h:266:75: note: in instantiation of member function 'std::unique_ptr<Dist<CppAD::AD<double>>>::reset' requested here
266 | _LIBCPP_INLINE_VISIBILITY _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));
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/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:1040:28: warning: variables 'i' and 'dim' used in loop condition not modified in loop body [-Wfor-loop-analysis]
1040 | for(int i = j + 1; i < dim; j++) {
| ^ ~~~
./dist_def.hpp:1000:3: note: in instantiation of member function 'MultivariateNormal<double>::link' requested here
1000 | MultivariateNormal() {};
| ^
./dist.hpp:36:44: note: in instantiation of member function 'MultivariateNormal<double>::MultivariateNormal' requested here
36 | 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));
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/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 /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/TMB/include/TMB.hpp:46:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/TMB/include/Rstream.hpp:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/ios:222:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__locale:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__memory/shared_ptr.h:31:
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__memory/unique_ptr.h:68:5: warning: delete called on 'Dist<double>' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
68 | delete __ptr;
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__memory/unique_ptr.h:300:7: note: in instantiation of member function 'std::default_delete<Dist<double>>::operator()' requested here
300 | __ptr_.second()(__tmp);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__memory/unique_ptr.h:266:75: note: in instantiation of member function 'std::unique_ptr<Dist<double>>::reset' requested here
266 | _LIBCPP_INLINE_VISIBILITY _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));
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/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:1040:28: warning: variables 'i' and 'dim' used in loop condition not modified in loop body [-Wfor-loop-analysis]
1040 | for(int i = j + 1; i < dim; j++) {
| ^ ~~~
./dist_def.hpp:1000:3: note: in instantiation of member function 'MultivariateNormal<CppAD::AD<CppAD::AD<double>>>::link' requested here
1000 | MultivariateNormal() {};
| ^
./dist.hpp:36:44: note: in instantiation of member function 'MultivariateNormal<CppAD::AD<CppAD::AD<double>>>::MultivariateNormal' requested here
36 | 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));
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/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()();
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/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 /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/TMB/include/TMB.hpp:46:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/TMB/include/Rstream.hpp:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/ios:222:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__locale:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__memory/shared_ptr.h:31:
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__memory/unique_ptr.h:68:5: warning: delete called on 'Dist<CppAD::AD<CppAD::AD<double>>>' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
68 | delete __ptr;
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__memory/unique_ptr.h:300:7: note: in instantiation of member function 'std::default_delete<Dist<CppAD::AD<CppAD::AD<double>>>>::operator()' requested here
300 | __ptr_.second()(__tmp);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__memory/unique_ptr.h:266:75: note: in instantiation of member function 'std::unique_ptr<Dist<CppAD::AD<CppAD::AD<double>>>>::reset' requested here
266 | _LIBCPP_INLINE_VISIBILITY _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));
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/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()();
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/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:1040:28: warning: variables 'i' and 'dim' used in loop condition not modified in loop body [-Wfor-loop-analysis]
1040 | for(int i = j + 1; i < dim; j++) {
| ^ ~~~
./dist_def.hpp:1000:3: note: in instantiation of member function 'MultivariateNormal<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>::link' requested here
1000 | MultivariateNormal() {};
| ^
./dist.hpp:36:44: note: in instantiation of member function 'MultivariateNormal<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>::MultivariateNormal' requested here
36 | 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));
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/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()();
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/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 /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/TMB/include/TMB.hpp:46:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/TMB/include/Rstream.hpp:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/ios:222:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__locale:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__memory/shared_ptr.h:31:
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__memory/unique_ptr.h:68:5: 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]
68 | delete __ptr;
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__memory/unique_ptr.h:300:7: note: in instantiation of member function 'std::default_delete<Dist<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>>::operator()' requested here
300 | __ptr_.second()(__tmp);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__memory/unique_ptr.h:266:75: note: in instantiation of member function 'std::unique_ptr<Dist<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>>::reset' requested here
266 | _LIBCPP_INLINE_VISIBILITY _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));
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/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()();
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/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++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o hmmTMB.so hmmTMB.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Volumes/Builds/packages/sonoma-arm64/results/4.6/hmmTMB.Rcheck/00LOCK-hmmTMB/00new/hmmTMB/libs
** generating debug symbols (dSYM)
** 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)