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1: RcppArmad... (0.9.300.2.0 -> 0.9.400.2.0) [CRAN]
Enter one or more numbers separated by spaces, or an empty line to cancel 1: 1 RcppArmad... (0.9.300.2.0 -> 0.9.400.2.0) [CRAN]
The downloaded binary packages are in /var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T//RtmpqUkeZn/downloaded_packages ✔ checking for file ‘/private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/RtmpqUkeZn/remotes47145e93d68/emvolz-phylodynamics-phydynR-e3047a6/DESCRIPTION’ (390ms) ─ preparing ‘phydynR’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ installing the package to process help pages
─ installing source package ‘phydynR’ ... ** libs clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c colikModular0.cpp -o colikModular0.o colikModular0.cpp:89:6: warning: unused variable 'm' [-Wunused-variable] int m = Y.size(); ^ 1 warning generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c dAL0.cpp -o dAL0.o dAL0.cpp:30:12: warning: unused variable 'w' [-Wunused-variable] int k,l,z,w; ^ dAL0.cpp:30:10: warning: unused variable 'z' [-Wunused-variable] int k,l,z,w; ^ 2 warnings generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c dPikL0.cpp -o dPikL0.o In file included from dPikL0.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint.hpp:45: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint/stepper/bulirsch_stoer_dense_out.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/factorials.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/constants/constants.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/container_fwd.hpp:61: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace] BOOST_MOVE_STD_NS_BEG ^ /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^/Library/Developer/CommandLineTools/usr/include/c++/v1/__config:445:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^dPikL0.cpp:112:10: warning: unused variable 'steps' [-Wunused-variable] size_t steps = integrate( dpikl0 , x , h0 , h1 ^ dPikL0.cpp:28:9: warning: private field 'sumA' is not used [-Wunused-private-field] double sumA; ^ 3 warnings generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c dPikL1.cpp -o dPikL1.o In file included from dPikL1.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint.hpp:45: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint/stepper/bulirsch_stoer_dense_out.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/factorials.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/constants/constants.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/container_fwd.hpp:61: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace] BOOST_MOVE_STD_NS_BEG ^ /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^/Library/Developer/CommandLineTools/usr/include/c++/v1/__config:445:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^dPikL1.cpp:129:10: warning: unused variable 'steps' [-Wunused-variable] size_t steps = integrate( dpikl0 , x , h0 , h1 ^ dPikL1.cpp:28:9: warning: private field 'sumA' is not used [-Wunused-private-field] double sumA; ^ 3 warnings generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c dQALarma0.cpp -o dQALarma0.o dQALarma0.cpp:59:6: warning: unused variable 'Lind' [-Wunused-variable] int Lind = x.size(); ^ 1 warning generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c dQfwd.cpp -o dQfwd.o In file included from dQfwd.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint.hpp:45: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint/stepper/bulirsch_stoer_dense_out.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/factorials.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/constants/constants.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/container_fwd.hpp:61: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace] BOOST_MOVE_STD_NS_BEG ^ /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^/Library/Developer/CommandLineTools/usr/include/c++/v1/__config:445:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^dQfwd.cpp:46:13: warning: unused variable 'w' [-Wunused-variable] int k,l,z,w; ^ dQfwd.cpp:127:9: warning: unused variable 'steps' [-Wunused-variable] size_t steps = boost::numeric::odeint::integrate( dqfwd , x , t0 , t1 ^ dQfwd.cpp:29:9: warning: private field 'sumA' is not used [-Wunused-private-field] double sumA; ^ 4 warnings generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c phylo.source.attribution.cpp -o phylo.source.attribution.o In file included from phylo.source.attribution.cpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint.hpp:45: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint/stepper/bulirsch_stoer_dense_out.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/factorials.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/constants/constants.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/container_fwd.hpp:61: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace] BOOST_MOVE_STD_NS_BEG ^ /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^/Library/Developer/CommandLineTools/usr/include/c++/v1/__config:445:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^phylo.source.attribution.cpp:67:212: warning: field 'nextant_tip' is uninitialized when used here [-Wuninitialized] DPikRhoPsi( const List Fs, const List Gs, const List Ys, const int m, const double hres, const double treeT, const int nextant) : Fs(Fs),Gs(Gs),Ys(Ys),m(m),hres(hres),treeT(treeT),nextant(nextant),nextant_tip(nextant_tip) { }; ^ phylo.source.attribution.cpp:236:16: warning: unused variable 'h1' [-Wunused-variable] double h, h0, h1, hstar, dh; ^ phylo.source.attribution.cpp:236:12: warning: unused variable 'h0' [-Wunused-variable] double h, h0, h1, hstar, dh; ^ phylo.source.attribution.cpp:187:17: warning: unused variable 'k' [-Wunused-variable] int u,v,w,z,a, k, l; ^ phylo.source.attribution.cpp:236:27: warning: unused variable 'dh' [-Wunused-variable] double h, h0, h1, hstar, dh; ^ phylo.source.attribution.cpp:184:9: warning: unused variable 'loglik' [-Wunused-variable] double loglik = 0.; ^ phylo.source.attribution.cpp:187:20: warning: unused variable 'l' [-Wunused-variable] int u,v,w,z,a, k, l; ^ phylo.source.attribution.cpp:187:12: warning: unused variable 'z' [-Wunused-variable] int u,v,w,z,a, k, l; ^ phylo.source.attribution.cpp:235:9: warning: unused variable 'sterm0' [-Wunused-variable] double sterm0, sterm1; ^ phylo.source.attribution.cpp:235:17: warning: unused variable 'sterm1' [-Wunused-variable] double sterm0, sterm1; ^ phylo.source.attribution.cpp:236:20: warning: unused variable 'hstar' [-Wunused-variable] double h, h0, h1, hstar, dh; ^ phylo.source.attribution.cpp:187:10: warning: unused variable 'w' [-Wunused-variable] int u,v,w,z,a, k, l; ^ phylo.source.attribution.cpp:63:9: warning: private field 'sumA' is not used [-Wunused-private-field] double sumA; ^ 14 warnings generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c psa2.cpp -o psa2.o In file included from psa2.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint.hpp:45: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint/stepper/bulirsch_stoer_dense_out.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/factorials.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/constants/constants.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/container_fwd.hpp:61: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace] BOOST_MOVE_STD_NS_BEG ^ /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^/Library/Developer/CommandLineTools/usr/include/c++/v1/__config:445:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^psa2.cpp:92:13: warning: unused variable 'w' [-Wunused-variable] int k,l,z,w; ^ psa2.cpp:273:13: warning: unused variable 'w' [-Wunused-variable] int k,l,z,w; ^ psa2.cpp:416:20: warning: unused variable 'l' [-Wunused-variable] int u,v,w,z,a, k, l; ^ psa2.cpp:459:12: warning: unused variable 'h0' [-Wunused-variable] double h, h0, h1, hstar, dh; ^ psa2.cpp:459:16: warning: unused variable 'h1' [-Wunused-variable] double h, h0, h1, hstar, dh; ^ psa2.cpp:459:20: warning: unused variable 'hstar' [-Wunused-variable] double h, h0, h1, hstar, dh; ^ psa2.cpp:459:27: warning: unused variable 'dh' [-Wunused-variable] double h, h0, h1, hstar, dh; ^ psa2.cpp:458:17: warning: unused variable 'sterm1' [-Wunused-variable] double sterm0, sterm1; ^ psa2.cpp:458:9: warning: unused variable 'sterm0' [-Wunused-variable] double sterm0, sterm1; ^ psa2.cpp:416:10: warning: unused variable 'w' [-Wunused-variable] int u,v,w,z,a, k, l; ^ psa2.cpp:416:12: warning: unused variable 'z' [-Wunused-variable] int u,v,w,z,a, k, l; ^ psa2.cpp:412:9: warning: unused variable 'loglik' [-Wunused-variable] double loglik = 0.; ^ psa2.cpp:416:17: warning: unused variable 'k' [-Wunused-variable] int u,v,w,z,a, k, l; ^ psa2.cpp:16:18: warning: unused variable 'CO' [-Wunused-const-variable] static const int CO = 1; ^ 15 warnings generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c solveQALboost0.cpp -o solveQALboost0.o In file included from solveQALboost0.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint.hpp:45: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint/stepper/bulirsch_stoer_dense_out.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/factorials.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/constants/constants.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/container_fwd.hpp:61: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace] BOOST_MOVE_STD_NS_BEG ^ /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^/Library/Developer/CommandLineTools/usr/include/c++/v1/__config:445:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^solveQALboost0.cpp:41:13: warning: unused variable 'w' [-Wunused-variable] int k,l,z,w; ^ solveQALboost0.cpp:215:13: warning: unused variable 'w' [-Wunused-variable] int k,l,z,w; ^ solveQALboost0.cpp:252:10: warning: unused variable 'Ydenom' [-Wunused-variable] double Ydenom; ^ solveQALboost0.cpp:353:9: warning: unused variable 'steps' [-Wunused-variable] size_t steps = boost::numeric::odeint::integrate( dqal , x , h0 , h1 ^ 5 warnings generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c solveQALboost1.cpp -o solveQALboost1.o In file included from solveQALboost1.cpp:9: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint.hpp:45: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint/stepper/bulirsch_stoer_dense_out.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/factorials.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/constants/constants.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/container_fwd.hpp:61: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace] BOOST_MOVE_STD_NS_BEG ^ /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^/Library/Developer/CommandLineTools/usr/include/c++/v1/__config:445:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^solveQALboost1.cpp:54:13: warning: unused variable 'w' [-Wunused-variable] int k,l,z,w; ^ solveQALboost1.cpp:79:10: warning: unused variable 'Ydenom' [-Wunused-variable] double Ydenom; ^ 3 warnings generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c treeSimulatorCpp2.cpp -o treeSimulatorCpp2.o treeSimulatorCpp2.cpp:101:12: warning: unused variable 't0' [-Wunused-variable] double t, t0, t1; ^ treeSimulatorCpp2.cpp:112:21: warning: unused variable 'nco' [-Wunused-variable] int it, ist, k, l, nco, inco , i, stateOf_a, stateOf_recip; ^ treeSimulatorCpp2.cpp:115:30: warning: unused variable 'twk' [-Wunused-variable] double r, rk, rl, cwk, cwl, twk, twl, h1; ^ treeSimulatorCpp2.cpp:115:25: warning: unused variable 'cwl' [-Wunused-variable] double r, rk, rl, cwk, cwl, twk, twl, h1; ^ treeSimulatorCpp2.cpp:112:26: warning: unused variable 'inco' [-Wunused-variable] int it, ist, k, l, nco, inco , i, stateOf_a, stateOf_recip; ^ treeSimulatorCpp2.cpp:115:20: warning: unused variable 'cwk' [-Wunused-variable] double r, rk, rl, cwk, cwl, twk, twl, h1; ^ treeSimulatorCpp2.cpp:137:15: warning: unused variable 'deltah' [-Wunused-variable] const double deltah = times[0] - times[1]; //note times decreasing ^ treeSimulatorCpp2.cpp:102:6: warning: unused variable 'internalNodeIndex' [-Wunused-variable] int internalNodeIndex = n; // counter for internal branches ^ treeSimulatorCpp2.cpp:112:47: warning: unused variable 'stateOf_recip' [-Wunused-variable] int it, ist, k, l, nco, inco , i, stateOf_a, stateOf_recip; ^ treeSimulatorCpp2.cpp:115:35: warning: unused variable 'twl' [-Wunused-variable] double r, rk, rl, cwk, cwl, twk, twl, h1; ^ treeSimulatorCpp2.cpp:112:36: warning: unused variable 'stateOf_a' [-Wunused-variable] int it, ist, k, l, nco, inco , i, stateOf_a, stateOf_recip; ^ treeSimulatorCpp2.cpp:81:9: warning: unused variable 'maxHeight' [-Wunused-variable] double maxHeight = maxSampleTime -tfin; ^ treeSimulatorCpp2.cpp:112:10: warning: unused variable 'ist' [-Wunused-variable] int it, ist, k, l, nco, inco , i, stateOf_a, stateOf_recip; ^ treeSimulatorCpp2.cpp:82:15: warning: unused variable 'deltat' [-Wunused-variable] const double deltat = times[0] - times[1]; ^ treeSimulatorCpp2.cpp:13:21: warning: unused variable 'A_EPS' [-Wunused-const-variable] static const double A_EPS = 0.00; ^ treeSimulatorCpp2.cpp:14:21: warning: unused variable 'Y_EPS' [-Wunused-const-variable] static const double Y_EPS = 1.E-12; ^ 16 warnings generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c treeSimulatorCpp3.cpp -o treeSimulatorCpp3.o treeSimulatorCpp3.cpp:197:7: warning: unused variable 'k' [-Wunused-variable] int k; ^ treeSimulatorCpp3.cpp:351:12: warning: assigning field to itself [-Wself-assign-field] for (u = u; u < (n + internalNodesAdded); u++){ ^ treeSimulatorCpp3.cpp:13:21: warning: unused variable 'A_EPS' [-Wunused-const-variable] static const double A_EPS = 0.00; ^ treeSimulatorCpp3.cpp:14:21: warning: unused variable 'Y_EPS' [-Wunused-const-variable] static const double Y_EPS = 1.E-12; ^ 4 warnings generated. clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o phydynR.so RcppExports.o colikModular0.o dAL0.o dPikL0.o dPikL1.o dQALarma0.o dQfwd.o phylo.source.attribution.o psa2.o solveQALboost0.o solveQALboost1.o treeSimulatorCpp2.o treeSimulatorCpp3.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' ld: warning: directory not found for option '-L/usr/local/gfortran/lib' ld: library not found for -lgfortran clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [phydynR.so] Error 1 ERROR: compilation failed for package ‘phydynR’ ─ removing ‘/private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/RtmpKZg2xv/Rinstbff6c4017d1/phydynR’
ERROR: package installation failed
install_github("emvolz-phylodynamics/phydynR") ✔ checking for file ‘/private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/RtmpqUkeZn/remotes47150a82f03/emvolz-phylodynamics-phydynR-e3047a6/DESCRIPTION’ ... ─ preparing ‘phydynR’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ installing the package to process help pages
─ installing source package ‘phydynR’ ... ** libs clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c colikModular0.cpp -o colikModular0.o colikModular0.cpp:89:6: warning: unused variable 'm' [-Wunused-variable] int m = Y.size(); ^ 1 warning generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c dAL0.cpp -o dAL0.o dAL0.cpp:30:12: warning: unused variable 'w' [-Wunused-variable] int k,l,z,w; ^ dAL0.cpp:30:10: warning: unused variable 'z' [-Wunused-variable] int k,l,z,w; ^ 2 warnings generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c dPikL0.cpp -o dPikL0.o In file included from dPikL0.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint.hpp:45: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint/stepper/bulirsch_stoer_dense_out.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/factorials.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/constants/constants.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/container_fwd.hpp:61: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace] BOOST_MOVE_STD_NS_BEG ^ /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^ /Library/Developer/CommandLineTools/usr/include/c++/v1/__config:445:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^ dPikL0.cpp:112:10: warning: unused variable 'steps' [-Wunused-variable] size_t steps = integrate( dpikl0 , x , h0 , h1 ^ dPikL0.cpp:28:9: warning: private field 'sumA' is not used [-Wunused-private-field] double sumA; ^ 3 warnings generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c dPikL1.cpp -o dPikL1.o In file included from dPikL1.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint.hpp:45: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint/stepper/bulirsch_stoer_dense_out.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/factorials.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/constants/constants.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/container_fwd.hpp:61: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace] BOOST_MOVE_STD_NS_BEG ^ /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^ /Library/Developer/CommandLineTools/usr/include/c++/v1/__config:445:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^ dPikL1.cpp:129:10: warning: unused variable 'steps' [-Wunused-variable] size_t steps = integrate( dpikl0 , x , h0 , h1 ^ dPikL1.cpp:28:9: warning: private field 'sumA' is not used [-Wunused-private-field] double sumA; ^ 3 warnings generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c dQALarma0.cpp -o dQALarma0.o dQALarma0.cpp:59:6: warning: unused variable 'Lind' [-Wunused-variable] int Lind = x.size(); ^ 1 warning generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c dQfwd.cpp -o dQfwd.o In file included from dQfwd.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint.hpp:45: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint/stepper/bulirsch_stoer_dense_out.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/factorials.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/constants/constants.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/container_fwd.hpp:61: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace] BOOST_MOVE_STD_NS_BEG ^ /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^ /Library/Developer/CommandLineTools/usr/include/c++/v1/__config:445:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^ dQfwd.cpp:46:13: warning: unused variable 'w' [-Wunused-variable] int k,l,z,w; ^ dQfwd.cpp:127:9: warning: unused variable 'steps' [-Wunused-variable] size_t steps = boost::numeric::odeint::integrate( dqfwd , x , t0 , t1 ^ dQfwd.cpp:29:9: warning: private field 'sumA' is not used [-Wunused-private-field] double sumA; ^ 4 warnings generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c phylo.source.attribution.cpp -o phylo.source.attribution.o In file included from phylo.source.attribution.cpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint.hpp:45: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint/stepper/bulirsch_stoer_dense_out.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/factorials.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/constants/constants.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/container_fwd.hpp:61: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace] BOOST_MOVE_STD_NS_BEG ^ /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^ /Library/Developer/CommandLineTools/usr/include/c++/v1/__config:445:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^ phylo.source.attribution.cpp:67:212: warning: field 'nextant_tip' is uninitialized when used here [-Wuninitialized] DPikRhoPsi( const List Fs, const List Gs, const List Ys, const int m, const double hres, const double treeT, const int nextant) : Fs(Fs),Gs(Gs),Ys(Ys),m(m),hres(hres),treeT(treeT),nextant(nextant),nextant_tip(nextant_tip) { }; ^ phylo.source.attribution.cpp:236:27: warning: unused variable 'dh' [-Wunused-variable] double h, h0, h1, hstar, dh; ^ phylo.source.attribution.cpp:236:20: warning: unused variable 'hstar' [-Wunused-variable] double h, h0, h1, hstar, dh; ^ phylo.source.attribution.cpp:236:16: warning: unused variable 'h1' [-Wunused-variable] double h, h0, h1, hstar, dh; ^ phylo.source.attribution.cpp:236:12: warning: unused variable 'h0' [-Wunused-variable] double h, h0, h1, hstar, dh; ^ phylo.source.attribution.cpp:235:9: warning: unused variable 'sterm0' [-Wunused-variable] double sterm0, sterm1; ^ phylo.source.attribution.cpp:235:17: warning: unused variable 'sterm1' [-Wunused-variable] double sterm0, sterm1; ^ phylo.source.attribution.cpp:187:10: warning: unused variable 'w' [-Wunused-variable] int u,v,w,z,a, k, l; ^ phylo.source.attribution.cpp:187:12: warning: unused variable 'z' [-Wunused-variable] int u,v,w,z,a, k, l; ^ phylo.source.attribution.cpp:187:17: warning: unused variable 'k' [-Wunused-variable] int u,v,w,z,a, k, l; ^ phylo.source.attribution.cpp:184:9: warning: unused variable 'loglik' [-Wunused-variable] double loglik = 0.; ^ phylo.source.attribution.cpp:187:20: warning: unused variable 'l' [-Wunused-variable] int u,v,w,z,a, k, l; ^ phylo.source.attribution.cpp:63:9: warning: private field 'sumA' is not used [-Wunused-private-field] double sumA; ^ 14 warnings generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c psa2.cpp -o psa2.o In file included from psa2.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint.hpp:45: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint/stepper/bulirsch_stoer_dense_out.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/factorials.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/constants/constants.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/container_fwd.hpp:61: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace] BOOST_MOVE_STD_NS_BEG ^ /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^ /Library/Developer/CommandLineTools/usr/include/c++/v1/__config:445:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^ psa2.cpp:92:13: warning: unused variable 'w' [-Wunused-variable] int k,l,z,w; ^ psa2.cpp:273:13: warning: unused variable 'w' [-Wunused-variable] int k,l,z,w; ^ psa2.cpp:416:20: warning: unused variable 'l' [-Wunused-variable] int u,v,w,z,a, k, l; ^ psa2.cpp:459:12: warning: unused variable 'h0' [-Wunused-variable] double h, h0, h1, hstar, dh; ^ psa2.cpp:459:16: warning: unused variable 'h1' [-Wunused-variable] double h, h0, h1, hstar, dh; ^ psa2.cpp:459:20: warning: unused variable 'hstar' [-Wunused-variable] double h, h0, h1, hstar, dh; ^ psa2.cpp:459:27: warning: unused variable 'dh' [-Wunused-variable] double h, h0, h1, hstar, dh; ^ psa2.cpp:458:17: warning: unused variable 'sterm1' [-Wunused-variable] double sterm0, sterm1; ^ psa2.cpp:458:9: warning: unused variable 'sterm0' [-Wunused-variable] double sterm0, sterm1; ^ psa2.cpp:416:10: warning: unused variable 'w' [-Wunused-variable] int u,v,w,z,a, k, l; ^ psa2.cpp:416:12: warning: unused variable 'z' [-Wunused-variable] int u,v,w,z,a, k, l; ^ psa2.cpp:412:9: warning: unused variable 'loglik' [-Wunused-variable] double loglik = 0.; ^ psa2.cpp:416:17: warning: unused variable 'k' [-Wunused-variable] int u,v,w,z,a, k, l; ^ psa2.cpp:16:18: warning: unused variable 'CO' [-Wunused-const-variable] static const int CO = 1; ^ 15 warnings generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c solveQALboost0.cpp -o solveQALboost0.o In file included from solveQALboost0.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint.hpp:45: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint/stepper/bulirsch_stoer_dense_out.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/factorials.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/constants/constants.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/container_fwd.hpp:61: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace] BOOST_MOVE_STD_NS_BEG ^ /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^ /Library/Developer/CommandLineTools/usr/include/c++/v1/__config:445:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^ solveQALboost0.cpp:41:13: warning: unused variable 'w' [-Wunused-variable] int k,l,z,w; ^ solveQALboost0.cpp:215:13: warning: unused variable 'w' [-Wunused-variable] int k,l,z,w; ^ solveQALboost0.cpp:252:10: warning: unused variable 'Ydenom' [-Wunused-variable] double Ydenom; ^ solveQALboost0.cpp:353:9: warning: unused variable 'steps' [-Wunused-variable] size_t steps = boost::numeric::odeint::integrate( dqal , x , h0 , h1 ^ 5 warnings generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c solveQALboost1.cpp -o solveQALboost1.o In file included from solveQALboost1.cpp:9: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint.hpp:45: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/numeric/odeint/stepper/bulirsch_stoer_dense_out.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/factorials.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/constants/constants.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/container_fwd.hpp:61: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace] BOOST_MOVE_STD_NS_BEG ^ /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^ /Library/Developer/CommandLineTools/usr/include/c++/v1/__config:445:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^ solveQALboost1.cpp:54:13: warning: unused variable 'w' [-Wunused-variable] int k,l,z,w; ^ solveQALboost1.cpp:79:10: warning: unused variable 'Ydenom' [-Wunused-variable] double Ydenom; ^ 3 warnings generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c treeSimulatorCpp2.cpp -o treeSimulatorCpp2.o treeSimulatorCpp2.cpp:112:47: warning: unused variable 'stateOf_recip' [-Wunused-variable] int it, ist, k, l, nco, inco , i, stateOf_a, stateOf_recip; ^ treeSimulatorCpp2.cpp:115:35: warning: unused variable 'twl' [-Wunused-variable] double r, rk, rl, cwk, cwl, twk, twl, h1; ^ treeSimulatorCpp2.cpp:101:12: warning: unused variable 't0' [-Wunused-variable] double t, t0, t1; ^ treeSimulatorCpp2.cpp:112:21: warning: unused variable 'nco' [-Wunused-variable] int it, ist, k, l, nco, inco , i, stateOf_a, stateOf_recip; ^ treeSimulatorCpp2.cpp:112:36: warning: unused variable 'stateOf_a' [-Wunused-variable] int it, ist, k, l, nco, inco , i, stateOf_a, stateOf_recip; ^ treeSimulatorCpp2.cpp:115:30: warning: unused variable 'twk' [-Wunused-variable] double r, rk, rl, cwk, cwl, twk, twl, h1; ^ treeSimulatorCpp2.cpp:115:25: warning: unused variable 'cwl' [-Wunused-variable] double r, rk, rl, cwk, cwl, twk, twl, h1; ^ treeSimulatorCpp2.cpp:112:26: warning: unused variable 'inco' [-Wunused-variable] int it, ist, k, l, nco, inco , i, stateOf_a, stateOf_recip; ^ treeSimulatorCpp2.cpp:115:20: warning: unused variable 'cwk' [-Wunused-variable] double r, rk, rl, cwk, cwl, twk, twl, h1; ^ treeSimulatorCpp2.cpp:102:6: warning: unused variable 'internalNodeIndex' [-Wunused-variable] int internalNodeIndex = n; // counter for internal branches ^ treeSimulatorCpp2.cpp:112:10: warning: unused variable 'ist' [-Wunused-variable] int it, ist, k, l, nco, inco , i, stateOf_a, stateOf_recip; ^ treeSimulatorCpp2.cpp:82:15: warning: unused variable 'deltat' [-Wunused-variable] const double deltat = times[0] - times[1]; ^ treeSimulatorCpp2.cpp:81:9: warning: unused variable 'maxHeight' [-Wunused-variable] double maxHeight = maxSampleTime -tfin; ^ treeSimulatorCpp2.cpp:137:15: warning: unused variable 'deltah' [-Wunused-variable] const double deltah = times[0] - times[1]; //note times decreasing ^ treeSimulatorCpp2.cpp:13:21: warning: unused variable 'A_EPS' [-Wunused-const-variable] static const double A_EPS = 0.00; ^ treeSimulatorCpp2.cpp:14:21: warning: unused variable 'Y_EPS' [-Wunused-const-variable] static const double Y_EPS = 1.E-12; ^ 16 warnings generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c treeSimulatorCpp3.cpp -o treeSimulatorCpp3.o treeSimulatorCpp3.cpp:197:7: warning: unused variable 'k' [-Wunused-variable] int k; ^ treeSimulatorCpp3.cpp:351:12: warning: assigning field to itself [-Wself-assign-field] for (u = u; u < (n + internalNodesAdded); u++){ ^ treeSimulatorCpp3.cpp:13:21: warning: unused variable 'A_EPS' [-Wunused-const-variable] static const double A_EPS = 0.00; ^ treeSimulatorCpp3.cpp:14:21: warning: unused variable 'Y_EPS' [-Wunused-const-variable] static const double Y_EPS = 1.E-12; ^ 4 warnings generated. clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o phydynR.so RcppExports.o colikModular0.o dAL0.o dPikL0.o dPikL1.o dQALarma0.o dQfwd.o phylo.source.attribution.o psa2.o solveQALboost0.o solveQALboost1.o treeSimulatorCpp2.o treeSimulatorCpp3.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' ld: warning: directory not found for option '-L/usr/local/gfortran/lib' ld: library not found for -lgfortran clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [phydynR.so] Error 1 ERROR: compilation failed for package ‘phydynR’ ─ removing ‘/private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/RtmpzGWQYP/Rinstc4e5b49cc32/phydynR’
ERROR: package installation failed
Error in library(phydynR) : there is no package called ‘phydynR’ Error in library(phydynR) : there is no package called ‘phydynR’ Error in library(phydynR) : there is no package called ‘phydynR’ Error in library(phydynR) : there is no package called ‘phydynR’ Error in library(phyland) : there is no package called ‘phyland’ Loading required package: ade4 Error in library(phydynR) : there is no package called ‘phydynR’ Error in plot$scales$clone() : attempt to apply non-function Error in plot$scales$clone() : attempt to apply non-function Error in plot$scales$clone() : attempt to apply non-function Error in plot$scales$clone() : attempt to apply non-function Error in phylandml(tre2, delimiter = NULL, regex = "camel|human", quiet = TRUE) : could not find function "phylandml" Error: object 'fit' not found Error: object 'fit' not found Error in library(phydynR) : there is no package called ‘phydynR’ Error in phylandml(tre2, delimiter = NULL, regex = "camel|human", quiet = TRUE) : could not find function "phylandml" Error: object 'fit' not found