* 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))" make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. using C++ compiler: ‘clang version 18.1.4’ make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/hmmTMB/src' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. /usr/local/clang18/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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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/clang18/bin/../include/c++/v1/iostream:43: In file included from /usr/local/clang18/bin/../include/c++/v1/ios:223: In file included from /usr/local/clang18/bin/../include/c++/v1/__locale:15: In file included from /usr/local/clang18/bin/../include/c++/v1/__memory/shared_ptr.h:33: /usr/local/clang18/bin/../include/c++/v1/__memory/unique_ptr.h:66:5: warning: delete called on 'Dist>' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor] 66 | delete __ptr; | ^ /usr/local/clang18/bin/../include/c++/v1/__memory/unique_ptr.h:266:7: note: in instantiation of member function 'std::default_delete>>::operator()' requested here 266 | __ptr_.second()(__tmp); | ^ /usr/local/clang18/bin/../include/c++/v1/__memory/unique_ptr.h:236:71: note: in instantiation of member function 'std::unique_ptr>>::reset' requested here 236 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX23 ~unique_ptr() { reset(); } | ^ ./hmmTMB.hpp:154:43: note: in instantiation of member function 'std::unique_ptr>>::~unique_ptr' requested here 154 | std::unique_ptr> obsdist = dist_generator(distcode(var)); | ^ /data/gannet/ripley/R/test-clang/TMB/include/tmb_core.hpp:1308:6: note: in instantiation of member function 'objective_function>::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/clang18/bin/../include/c++/v1/iostream:43: In file included from /usr/local/clang18/bin/../include/c++/v1/ios:223: In file included from /usr/local/clang18/bin/../include/c++/v1/__locale:15: In file included from /usr/local/clang18/bin/../include/c++/v1/__memory/shared_ptr.h:33: /usr/local/clang18/bin/../include/c++/v1/__memory/unique_ptr.h:66:5: warning: delete called on 'Dist' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor] 66 | delete __ptr; | ^ /usr/local/clang18/bin/../include/c++/v1/__memory/unique_ptr.h:266:7: note: in instantiation of member function 'std::default_delete>::operator()' requested here 266 | __ptr_.second()(__tmp); | ^ /usr/local/clang18/bin/../include/c++/v1/__memory/unique_ptr.h:236:71: note: in instantiation of member function 'std::unique_ptr>::reset' requested here 236 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX23 ~unique_ptr() { reset(); } | ^ ./hmmTMB.hpp:154:43: note: in instantiation of member function 'std::unique_ptr>::~unique_ptr' requested here 154 | std::unique_ptr> obsdist = dist_generator(distcode(var)); | ^ /data/gannet/ripley/R/test-clang/TMB/include/tmb_core.hpp:2031:34: note: in instantiation of member function 'objective_function::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/clang18/bin/../include/c++/v1/iostream:43: In file included from /usr/local/clang18/bin/../include/c++/v1/ios:223: In file included from /usr/local/clang18/bin/../include/c++/v1/__locale:15: In file included from /usr/local/clang18/bin/../include/c++/v1/__memory/shared_ptr.h:33: /usr/local/clang18/bin/../include/c++/v1/__memory/unique_ptr.h:66:5: warning: delete called on 'Dist>>' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor] 66 | delete __ptr; | ^ /usr/local/clang18/bin/../include/c++/v1/__memory/unique_ptr.h:266:7: note: in instantiation of member function 'std::default_delete>>>::operator()' requested here 266 | __ptr_.second()(__tmp); | ^ /usr/local/clang18/bin/../include/c++/v1/__memory/unique_ptr.h:236:71: note: in instantiation of member function 'std::unique_ptr>>>::reset' requested here 236 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX23 ~unique_ptr() { reset(); } | ^ ./hmmTMB.hpp:154:43: note: in instantiation of member function 'std::unique_ptr>>>::~unique_ptr' requested here 154 | std::unique_ptr> obsdist = dist_generator(distcode(var)); | ^ /data/gannet/ripley/R/test-clang/TMB/include/tmb_core.hpp:913:20: note: in instantiation of member function 'objective_function>>::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>>::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/clang18/bin/../include/c++/v1/iostream:43: In file included from /usr/local/clang18/bin/../include/c++/v1/ios:223: In file included from /usr/local/clang18/bin/../include/c++/v1/__locale:15: In file included from /usr/local/clang18/bin/../include/c++/v1/__memory/shared_ptr.h:33: /usr/local/clang18/bin/../include/c++/v1/__memory/unique_ptr.h:66:5: warning: delete called on 'Dist>>>' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor] 66 | delete __ptr; | ^ /usr/local/clang18/bin/../include/c++/v1/__memory/unique_ptr.h:266:7: note: in instantiation of member function 'std::default_delete>>>>::operator()' requested here 266 | __ptr_.second()(__tmp); | ^ /usr/local/clang18/bin/../include/c++/v1/__memory/unique_ptr.h:236:71: note: in instantiation of member function 'std::unique_ptr>>>>::reset' requested here 236 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX23 ~unique_ptr() { reset(); } | ^ ./hmmTMB.hpp:154:43: note: in instantiation of member function 'std::unique_ptr>>>>::~unique_ptr' requested here 154 | std::unique_ptr> obsdist = dist_generator(distcode(var)); | ^ /data/gannet/ripley/R/test-clang/TMB/include/tmb_core.hpp:913:20: note: in instantiation of member function 'objective_function>>>::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>>>::evalUserTemplate' requested here 2361 | y[0] = F.evalUserTemplate(); | ^ 7 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/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]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. 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)