* installing *source* package ‘hmmTMB’ ... ** 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 14.0.3 (clang-1403.0.22.14.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/TMB/include" -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_hmmTMB -DCPPAD_FRAMEWORK -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/TMB/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include' -I/opt/R/x86_64/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/big-sur-x86_64/Rlib/4.3/TMB/include/TMB.hpp:87: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/Sparse:26: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/SparseCore:61: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] Index count = 0; ^ In file included from hmmTMB.cpp:2: In file included from ./hmmTMB.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/TMB/include/TMB.hpp:87: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/Sparse:31: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/SparseLU:33: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 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 /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/TMB/include/TMB.hpp:112: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/TMB/include/cppad/cppad.hpp:34: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/TMB/include/cppad/ode_gear.hpp:489:6: warning: variable 'sign' set but not used [-Wunused-but-set-variable] int sign; ^ In file included from hmmTMB.cpp:2: In file included from ./hmmTMB.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/TMB/include/TMB.hpp:112: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/TMB/include/cppad/cppad.hpp:39: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/TMB/include/cppad/romberg_mul.hpp:277:10: warning: variable 'pow2' set but not used [-Wunused-but-set-variable] size_t pow2 = 1; ^ In file included from hmmTMB.cpp:2: In file included from ./hmmTMB.hpp:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/TMB/include/TMB.hpp:41: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/TMB/include/Rstream.hpp:10: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/iostream:37: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/ios:215: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__locale:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/string:506: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/string_view:175: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__string:57: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/algorithm:643: /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2084:5: warning: delete called on 'Dist>' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor] delete __ptr; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2345:7: note: in instantiation of member function 'std::default_delete>>::operator()' requested here __ptr_.second()(__tmp); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2299:19: note: in instantiation of member function 'std::unique_ptr>>::reset' requested here ~unique_ptr() { reset(); } ^ ./hmmTMB.hpp:154:43: note: in instantiation of member function 'std::unique_ptr>>::~unique_ptr' requested here std::unique_ptr> obsdist = dist_generator(distcode(var)); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/TMB/include/tmb_core.hpp:1308:6: note: in instantiation of member function 'objective_function>::operator()' requested here 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/big-sur-x86_64/Rlib/4.3/TMB/include/TMB.hpp:41: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/TMB/include/Rstream.hpp:10: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/iostream:37: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/ios:215: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__locale:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/string:506: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/string_view:175: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__string:57: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/algorithm:643: /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2084:5: warning: delete called on 'Dist' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor] delete __ptr; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2345:7: note: in instantiation of member function 'std::default_delete>::operator()' requested here __ptr_.second()(__tmp); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2299:19: note: in instantiation of member function 'std::unique_ptr>::reset' requested here ~unique_ptr() { reset(); } ^ ./hmmTMB.hpp:154:43: note: in instantiation of member function 'std::unique_ptr>::~unique_ptr' requested here std::unique_ptr> obsdist = dist_generator(distcode(var)); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/TMB/include/tmb_core.hpp:2031:34: note: in instantiation of member function 'objective_function::operator()' requested here 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/big-sur-x86_64/Rlib/4.3/TMB/include/TMB.hpp:41: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/TMB/include/Rstream.hpp:10: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/iostream:37: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/ios:215: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__locale:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/string:506: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/string_view:175: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__string:57: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/algorithm:643: /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2084:5: warning: delete called on 'Dist>>' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor] delete __ptr; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2345:7: note: in instantiation of member function 'std::default_delete>>>::operator()' requested here __ptr_.second()(__tmp); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2299:19: note: in instantiation of member function 'std::unique_ptr>>>::reset' requested here ~unique_ptr() { reset(); } ^ ./hmmTMB.hpp:154:43: note: in instantiation of member function 'std::unique_ptr>>>::~unique_ptr' requested here std::unique_ptr> obsdist = dist_generator(distcode(var)); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/TMB/include/tmb_core.hpp:913:20: note: in instantiation of member function 'objective_function>>::operator()' requested here Type ans=this->operator()(); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/TMB/include/tmb_core.hpp:2112:10: note: in instantiation of member function 'objective_function>>::evalUserTemplate' requested here 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/big-sur-x86_64/Rlib/4.3/TMB/include/TMB.hpp:41: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/TMB/include/Rstream.hpp:10: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/iostream:37: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/ios:215: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__locale:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/string:506: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/string_view:175: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__string:57: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/algorithm:643: /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2084:5: warning: delete called on 'Dist>>>' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor] delete __ptr; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2345:7: note: in instantiation of member function 'std::default_delete>>>>::operator()' requested here __ptr_.second()(__tmp); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2299:19: note: in instantiation of member function 'std::unique_ptr>>>>::reset' requested here ~unique_ptr() { reset(); } ^ ./hmmTMB.hpp:154:43: note: in instantiation of member function 'std::unique_ptr>>>>::~unique_ptr' requested here std::unique_ptr> obsdist = dist_generator(distcode(var)); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/TMB/include/tmb_core.hpp:913:20: note: in instantiation of member function 'objective_function>>>::operator()' requested here Type ans=this->operator()(); ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/TMB/include/tmb_core.hpp:2361:12: note: in instantiation of member function 'objective_function>>>::evalUserTemplate' requested here y[0] = F.evalUserTemplate(); ^ 9 warnings generated. clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o hmmTMB.so hmmTMB.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation Warning message: In checkMatrixPackageVersion() : Package version inconsistency detected. TMB was built with Matrix version 1.6.0 Current Matrix version is 1.6.1.1 Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hmmTMB.Rcheck/00LOCK-hmmTMB/00new/hmmTMB/libs ** generating debug symbols (dSYM) ** R ** inst ** byte-compile and prepare package for lazy loading Warning message: In checkMatrixPackageVersion() : Package version inconsistency detected. TMB was built with Matrix version 1.6.0 Current Matrix version is 1.6.1.1 Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in checkMatrixPackageVersion() : Package version inconsistency detected. TMB was built with Matrix version 1.6.0 Current Matrix version is 1.6.1.1 Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning in checkMatrixPackageVersion() : Package version inconsistency detected. TMB was built with Matrix version 1.6.0 Current Matrix version is 1.6.1.1 Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package ** testing if installed package keeps a record of temporary installation path * DONE (hmmTMB)