* 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 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘NA’
clang++ -arch x86_64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include" -I"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_hmmTMB -DCPPAD_FRAMEWORK -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/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/4.6/TMB/include/TMB.hpp:96:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:26:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/RcppEigen/include/Eigen/SparseCore:61:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/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/4.6/TMB/include/TMB.hpp:96:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:29:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/RcppEigen/include/Eigen/SparseLU:35:
/Volumes/Builds/packages/big-sur-x86_64/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]
Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
^
/Volumes/Builds/packages/big-sur-x86_64/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]
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]
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
MultivariateNormal() {};
^
./dist.hpp:36:44: note: in instantiation of member function 'MultivariateNormal<CppAD::AD<double>>::MultivariateNormal' requested here
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
std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tmb_core.hpp:1312:6: note: in instantiation of member function 'objective_function<CppAD::AD<double>>::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/4.6/TMB/include/TMB.hpp:226:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:29:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/bessel/bessel.hpp:100:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/bessel/bessel_i.cpp:63:17: warning: ISO C++20 considers use of overloaded operator '==' (with operand types 'atomic::tiny_ad::variable<1, 2>' and 'atomic::tiny_ad::variable<1, 2>') to be ambiguous despite there being a unique best viable function [-Wambiguous-reversed-operator]
((alpha == na) ? /* sin(pi * alpha) = 0 */ 0 :
~~~~~ ^ ~~
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:40:17: note: in instantiation of function template specialization 'atomic::bessel_utils::bessel_i<atomic::tiny_ad::variable<1, 2>>' requested here
bessel_utils::bessel_i(x[0], x[1], 1.) )
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:38:17: note: in instantiation of function template specialization 'atomic::bessel_i<double>' requested here
TMB_BIND_ATOMIC(bessel_i,
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:38:1: note: in instantiation of member function 'atomic::atomicbessel_i<double>::forward' requested here
TMB_BIND_ATOMIC(bessel_i,
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/mask.hpp:73:45: note: expanded from macro 'TMB_BIND_ATOMIC'
#define TMB_BIND_ATOMIC(NAME,MASK,CALL) \
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/atomic_macro.hpp:85:38: note: expanded from macro '\
TMB_ATOMIC_VECTOR_FUNCTION'
static atomic##ATOMIC_NAME<Type> afun##ATOMIC_NAME( \
^
<scratch space>:63:1: note: expanded from here
afunbessel_i
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:38:17: note: in instantiation of function template specialization 'atomic::bessel_i<double>' requested here
TMB_BIND_ATOMIC(bessel_i,
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/distributions_R.hpp:495:19: note: in instantiation of function template specialization 'atomic::bessel_i<double>' requested here
ans = atomic::bessel_i(tx)[0];
^
./dist_def.hpp:952:14: note: in instantiation of function template specialization 'besselI<CppAD::AD<double>>' requested here
Type b = besselI(Type(par(1)), Type(0));
^
./dist_def.hpp:930:3: note: in instantiation of member function 'VonMises<CppAD::AD<double>>::pdf' requested here
VonMises() {};
^
./dist.hpp:52:44: note: in instantiation of member function 'VonMises<CppAD::AD<double>>::VonMises' requested here
return(std::unique_ptr<Dist<Type>>(new VonMises<Type>));
^
./hmmTMB.hpp:165:44: note: in instantiation of function template specialization 'dist_generator<CppAD::AD<double>>' requested here
std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tmb_core.hpp:1312:6: note: in instantiation of member function 'objective_function<CppAD::AD<double>>::operator()' requested here
F(); // Run through user template (modifies reportvector)
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/tiny_ad/tiny_ad.hpp:69:5: note: ambiguity is between a regular call to this operator and a call with the argument order reversed
COMPARISON_OPERATOR(==)
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/tiny_ad/tiny_ad.hpp:62:10: note: expanded from macro 'COMPARISON_OPERATOR'
bool operator OP (const other &x) const{ \
^
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/4.6/TMB/include/TMB.hpp:226:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:29:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/bessel/bessel.hpp:100:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/bessel/bessel_i.cpp:63:17: warning: ISO C++20 considers use of overloaded operator '==' (with operand types 'atomic::tiny_ad::variable<2, 2>' and 'atomic::tiny_ad::variable<2, 2>') to be ambiguous despite there being a unique best viable function [-Wambiguous-reversed-operator]
((alpha == na) ? /* sin(pi * alpha) = 0 */ 0 :
~~~~~ ^ ~~
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:40:17: note: in instantiation of function template specialization 'atomic::bessel_utils::bessel_i<atomic::tiny_ad::variable<2, 2>>' requested here
bessel_utils::bessel_i(x[0], x[1], 1.) )
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:38:17: note: in instantiation of function template specialization 'atomic::bessel_i<double>' requested here
TMB_BIND_ATOMIC(bessel_i,
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:38:1: note: in instantiation of member function 'atomic::atomicbessel_i<double>::forward' requested here
TMB_BIND_ATOMIC(bessel_i,
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/mask.hpp:73:45: note: expanded from macro 'TMB_BIND_ATOMIC'
#define TMB_BIND_ATOMIC(NAME,MASK,CALL) \
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/atomic_macro.hpp:85:38: note: expanded from macro '\
TMB_ATOMIC_VECTOR_FUNCTION'
static atomic##ATOMIC_NAME<Type> afun##ATOMIC_NAME( \
^
<scratch space>:63:1: note: expanded from here
afunbessel_i
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:38:17: note: in instantiation of function template specialization 'atomic::bessel_i<double>' requested here
TMB_BIND_ATOMIC(bessel_i,
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/distributions_R.hpp:495:19: note: in instantiation of function template specialization 'atomic::bessel_i<double>' requested here
ans = atomic::bessel_i(tx)[0];
^
./dist_def.hpp:952:14: note: in instantiation of function template specialization 'besselI<CppAD::AD<double>>' requested here
Type b = besselI(Type(par(1)), Type(0));
^
./dist_def.hpp:930:3: note: in instantiation of member function 'VonMises<CppAD::AD<double>>::pdf' requested here
VonMises() {};
^
./dist.hpp:52:44: note: in instantiation of member function 'VonMises<CppAD::AD<double>>::VonMises' requested here
return(std::unique_ptr<Dist<Type>>(new VonMises<Type>));
^
./hmmTMB.hpp:165:44: note: in instantiation of function template specialization 'dist_generator<CppAD::AD<double>>' requested here
std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tmb_core.hpp:1312:6: note: in instantiation of member function 'objective_function<CppAD::AD<double>>::operator()' requested here
F(); // Run through user template (modifies reportvector)
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/tiny_ad/tiny_ad.hpp:69:5: note: ambiguity is between a regular call to this operator and a call with the argument order reversed
COMPARISON_OPERATOR(==)
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/tiny_ad/tiny_ad.hpp:62:10: note: expanded from macro 'COMPARISON_OPERATOR'
bool operator OP (const other &x) const{ \
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/tiny_ad/tiny_ad.hpp:69:25: error: use of overloaded operator '==' is ambiguous (with operand types 'const atomic::tiny_ad::variable<1, 2>' and 'const atomic::tiny_ad::variable<2, 2>')
COMPARISON_OPERATOR(==)
~~~~~~~~~~~~~~~~~~~~^~~
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/tiny_ad/tiny_ad.hpp:63:21: note: expanded from macro 'COMPARISON_OPERATOR'
return (value OP x); \
~~~~~ ^ ~
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/bessel/bessel_i.cpp:63:17: note: in instantiation of function template specialization 'atomic::tiny_ad::ad<atomic::tiny_ad::variable<1, 2>, atomic::tiny_vec<atomic::tiny_ad::variable<1, 2>, 2>>::operator==<atomic::tiny_ad::variable<2, 2>>' requested here
((alpha == na) ? /* sin(pi * alpha) = 0 */ 0 :
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:40:17: note: in instantiation of function template specialization 'atomic::bessel_utils::bessel_i<atomic::tiny_ad::variable<2, 2>>' requested here
bessel_utils::bessel_i(x[0], x[1], 1.) )
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:38:17: note: in instantiation of function template specialization 'atomic::bessel_i<double>' requested here
TMB_BIND_ATOMIC(bessel_i,
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:38:1: note: in instantiation of member function 'atomic::atomicbessel_i<double>::forward' requested here
TMB_BIND_ATOMIC(bessel_i,
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/mask.hpp:73:45: note: expanded from macro 'TMB_BIND_ATOMIC'
#define TMB_BIND_ATOMIC(NAME,MASK,CALL) \
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/atomic_macro.hpp:85:38: note: expanded from macro '\
TMB_ATOMIC_VECTOR_FUNCTION'
static atomic##ATOMIC_NAME<Type> afun##ATOMIC_NAME( \
^
<scratch space>:63:1: note: expanded from here
afunbessel_i
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:38:17: note: in instantiation of function template specialization 'atomic::bessel_i<double>' requested here
TMB_BIND_ATOMIC(bessel_i,
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/distributions_R.hpp:495:19: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
ans = atomic::bessel_i(tx)[0];
^
./dist_def.hpp:952:14: note: in instantiation of function template specialization 'besselI<CppAD::AD<double>>' requested here
Type b = besselI(Type(par(1)), Type(0));
^
./dist_def.hpp:930:3: note: in instantiation of member function 'VonMises<CppAD::AD<double>>::pdf' requested here
VonMises() {};
^
./dist.hpp:52:44: note: in instantiation of member function 'VonMises<CppAD::AD<double>>::VonMises' requested here
return(std::unique_ptr<Dist<Type>>(new VonMises<Type>));
^
./hmmTMB.hpp:165:44: note: in instantiation of function template specialization 'dist_generator<CppAD::AD<double>>' requested here
std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tmb_core.hpp:1312:6: note: in instantiation of member function 'objective_function<CppAD::AD<double>>::operator()' requested here
F(); // Run through user template (modifies reportvector)
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/tiny_ad/tiny_ad.hpp:69:5: note: candidate function [with other = atomic::tiny_ad::variable<2, 2>]
COMPARISON_OPERATOR(==)
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/tiny_ad/tiny_ad.hpp:62:10: note: expanded from macro 'COMPARISON_OPERATOR'
bool operator OP (const other &x) const{ \
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/tiny_ad/tiny_ad.hpp:69:5: note: candidate function (with reversed parameter order) [with other = atomic::tiny_ad::variable<1, 2>]
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/tiny_ad/tiny_ad.hpp:62:10: note: expanded from macro 'COMPARISON_OPERATOR'
bool operator OP (const other &x) const{ \
^
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/4.6/TMB/include/TMB.hpp:226:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:29:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/bessel/bessel.hpp:100:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/bessel/bessel_i.cpp:63:17: warning: ISO C++20 considers use of overloaded operator '==' (with operand types 'atomic::tiny_ad::variable<3, 2>' and 'atomic::tiny_ad::variable<3, 2>') to be ambiguous despite there being a unique best viable function [-Wambiguous-reversed-operator]
((alpha == na) ? /* sin(pi * alpha) = 0 */ 0 :
~~~~~ ^ ~~
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:40:17: note: in instantiation of function template specialization 'atomic::bessel_utils::bessel_i<atomic::tiny_ad::variable<3, 2>>' requested here
bessel_utils::bessel_i(x[0], x[1], 1.) )
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:38:17: note: in instantiation of function template specialization 'atomic::bessel_i<double>' requested here
TMB_BIND_ATOMIC(bessel_i,
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:38:1: note: in instantiation of member function 'atomic::atomicbessel_i<double>::forward' requested here
TMB_BIND_ATOMIC(bessel_i,
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/mask.hpp:73:45: note: expanded from macro 'TMB_BIND_ATOMIC'
#define TMB_BIND_ATOMIC(NAME,MASK,CALL) \
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/atomic_macro.hpp:85:38: note: expanded from macro '\
TMB_ATOMIC_VECTOR_FUNCTION'
static atomic##ATOMIC_NAME<Type> afun##ATOMIC_NAME( \
^
<scratch space>:63:1: note: expanded from here
afunbessel_i
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:38:17: note: in instantiation of function template specialization 'atomic::bessel_i<double>' requested here
TMB_BIND_ATOMIC(bessel_i,
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/distributions_R.hpp:495:19: note: in instantiation of function template specialization 'atomic::bessel_i<double>' requested here
ans = atomic::bessel_i(tx)[0];
^
./dist_def.hpp:952:14: note: in instantiation of function template specialization 'besselI<CppAD::AD<double>>' requested here
Type b = besselI(Type(par(1)), Type(0));
^
./dist_def.hpp:930:3: note: in instantiation of member function 'VonMises<CppAD::AD<double>>::pdf' requested here
VonMises() {};
^
./dist.hpp:52:44: note: in instantiation of member function 'VonMises<CppAD::AD<double>>::VonMises' requested here
return(std::unique_ptr<Dist<Type>>(new VonMises<Type>));
^
./hmmTMB.hpp:165:44: note: in instantiation of function template specialization 'dist_generator<CppAD::AD<double>>' requested here
std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tmb_core.hpp:1312:6: note: in instantiation of member function 'objective_function<CppAD::AD<double>>::operator()' requested here
F(); // Run through user template (modifies reportvector)
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/tiny_ad/tiny_ad.hpp:69:5: note: ambiguity is between a regular call to this operator and a call with the argument order reversed
COMPARISON_OPERATOR(==)
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/tiny_ad/tiny_ad.hpp:62:10: note: expanded from macro 'COMPARISON_OPERATOR'
bool operator OP (const other &x) const{ \
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/tiny_ad/tiny_ad.hpp:69:25: error: use of overloaded operator '==' is ambiguous (with operand types 'const atomic::tiny_ad::variable<2, 2>' and 'const atomic::tiny_ad::variable<3, 2>')
COMPARISON_OPERATOR(==)
~~~~~~~~~~~~~~~~~~~~^~~
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/tiny_ad/tiny_ad.hpp:63:21: note: expanded from macro 'COMPARISON_OPERATOR'
return (value OP x); \
~~~~~ ^ ~
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/bessel/bessel_i.cpp:63:17: note: in instantiation of function template specialization 'atomic::tiny_ad::ad<atomic::tiny_ad::variable<2, 2>, atomic::tiny_vec<atomic::tiny_ad::variable<2, 2>, 2>>::operator==<atomic::tiny_ad::variable<3, 2>>' requested here
((alpha == na) ? /* sin(pi * alpha) = 0 */ 0 :
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:40:17: note: in instantiation of function template specialization 'atomic::bessel_utils::bessel_i<atomic::tiny_ad::variable<3, 2>>' requested here
bessel_utils::bessel_i(x[0], x[1], 1.) )
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:38:17: note: in instantiation of function template specialization 'atomic::bessel_i<double>' requested here
TMB_BIND_ATOMIC(bessel_i,
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:38:1: note: in instantiation of member function 'atomic::atomicbessel_i<double>::forward' requested here
TMB_BIND_ATOMIC(bessel_i,
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/mask.hpp:73:45: note: expanded from macro 'TMB_BIND_ATOMIC'
#define TMB_BIND_ATOMIC(NAME,MASK,CALL) \
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/atomic_macro.hpp:85:38: note: expanded from macro '\
TMB_ATOMIC_VECTOR_FUNCTION'
static atomic##ATOMIC_NAME<Type> afun##ATOMIC_NAME( \
^
<scratch space>:63:1: note: expanded from here
afunbessel_i
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/atomic.hpp:38:17: note: in instantiation of function template specialization 'atomic::bessel_i<double>' requested here
TMB_BIND_ATOMIC(bessel_i,
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/distributions_R.hpp:495:19: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
ans = atomic::bessel_i(tx)[0];
^
./dist_def.hpp:952:14: note: in instantiation of function template specialization 'besselI<CppAD::AD<double>>' requested here
Type b = besselI(Type(par(1)), Type(0));
^
./dist_def.hpp:930:3: note: in instantiation of member function 'VonMises<CppAD::AD<double>>::pdf' requested here
VonMises() {};
^
./dist.hpp:52:44: note: in instantiation of member function 'VonMises<CppAD::AD<double>>::VonMises' requested here
return(std::unique_ptr<Dist<Type>>(new VonMises<Type>));
^
./hmmTMB.hpp:165:44: note: in instantiation of function template specialization 'dist_generator<CppAD::AD<double>>' requested here
std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tmb_core.hpp:1312:6: note: in instantiation of member function 'objective_function<CppAD::AD<double>>::operator()' requested here
F(); // Run through user template (modifies reportvector)
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/tiny_ad/tiny_ad.hpp:69:5: note: candidate function [with other = atomic::tiny_ad::variable<3, 2>]
COMPARISON_OPERATOR(==)
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/tiny_ad/tiny_ad.hpp:62:10: note: expanded from macro 'COMPARISON_OPERATOR'
bool operator OP (const other &x) const{ \
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/tiny_ad/tiny_ad.hpp:69:5: note: candidate function (with reversed parameter order) [with other = atomic::tiny_ad::variable<2, 2>]
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tiny_ad/tiny_ad/tiny_ad.hpp:62:10: note: expanded from macro 'COMPARISON_OPERATOR'
bool operator OP (const other &x) const{ \
^
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/4.6/TMB/include/TMB.hpp:46:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/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<CppAD::AD<double>>' 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<Dist<CppAD::AD<double>>>::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<Dist<CppAD::AD<double>>>::reset' requested here
~unique_ptr() { reset(); }
^
./hmmTMB.hpp:165:44: note: in instantiation of member function 'std::unique_ptr<Dist<CppAD::AD<double>>>::~unique_ptr' requested here
std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tmb_core.hpp:1312:6: note: in instantiation of member function 'objective_function<CppAD::AD<double>>::operator()' requested here
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]
for(int i = j + 1; i < dim; j++) {
^ ~~~
./dist_def.hpp:1000:3: note: in instantiation of member function 'MultivariateNormal<double>::link' requested here
MultivariateNormal() {};
^
./dist.hpp:36:44: note: in instantiation of member function 'MultivariateNormal<double>::MultivariateNormal' requested here
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
std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tmb_core.hpp:2035:34: note: in instantiation of member function 'objective_function<double>::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/4.6/TMB/include/TMB.hpp:46:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/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<double>' 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<Dist<double>>::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<Dist<double>>::reset' requested here
~unique_ptr() { reset(); }
^
./hmmTMB.hpp:165:44: note: in instantiation of member function 'std::unique_ptr<Dist<double>>::~unique_ptr' requested here
std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/TMB/include/tmb_core.hpp:2035:34: note: in instantiation of member function 'objective_function<double>::operator()' requested here
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]
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
MultivariateNormal() {};
^
./dist.hpp:36:44: note: in instantiation of member function 'MultivariateNormal<CppAD::AD<CppAD::AD<double>>>::MultivariateNormal' requested here
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
std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
^
/Volumes/Builds/packages/big-sur-x86_64/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
Type ans=this->operator()();
^
/Volumes/Builds/packages/big-sur-x86_64/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
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/4.6/TMB/include/TMB.hpp:46:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/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<CppAD::AD<CppAD::AD<double>>>' 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<Dist<CppAD::AD<CppAD::AD<double>>>>::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<Dist<CppAD::AD<CppAD::AD<double>>>>::reset' requested here
~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
std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
^
/Volumes/Builds/packages/big-sur-x86_64/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
Type ans=this->operator()();
^
/Volumes/Builds/packages/big-sur-x86_64/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
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]
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
MultivariateNormal() {};
^
./dist.hpp:36:44: note: in instantiation of member function 'MultivariateNormal<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>::MultivariateNormal' requested here
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
std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
^
/Volumes/Builds/packages/big-sur-x86_64/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
Type ans=this->operator()();
^
/Volumes/Builds/packages/big-sur-x86_64/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
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/4.6/TMB/include/TMB.hpp:46:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/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<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>' 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<Dist<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>>::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<Dist<CppAD::AD<CppAD::AD<CppAD::AD<double>>>>>::reset' requested here
~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
std::unique_ptr<Dist<Type>> obsdist = dist_generator<Type>(distcode(var));
^
/Volumes/Builds/packages/big-sur-x86_64/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
Type ans=this->operator()();
^
/Volumes/Builds/packages/big-sur-x86_64/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
y[0] = F.evalUserTemplate();
^
14 warnings and 2 errors generated.
make[1]: *** [hmmTMB.o] Error 1
Error in TMB::compile("hmmTMB.cpp", safebounds = FALSE, safeunload = FALSE) :
Compilation failed
In addition: Warning message:
In system2("xcrun", "--show-sdk-version", TRUE, TRUE) :
running command ''xcrun' --show-sdk-version 2>&1' had status 1
Execution halted
make: *** [hmmTMB.so] Error 1
ERROR: compilation failed for package ‘hmmTMB’
* removing ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.6/hmmTMB.Rcheck/hmmTMB’