* installing *source* package ‘groupedSurv’ ...
** package ‘groupedSurv’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (GCC) 13.2.0’
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/groupedSurv/src'
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c Cuhre.c -o Cuhre.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c alphaEst.cpp -o alphaEst.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c betaEst.cpp -o betaEst.o
In file included from integrand_est.h:9,
from fam_LLBeta.h:11,
from betaEst.cpp:17:
global.h:18:35: warning: 'global_alpha_index_' defined but not used [-Wunused-variable]
18 | *global_alpha_index_,
| ^~~~~~~~~~~~~~~~~~~
global.h:16:35: warning: 'global_alpha_size_' defined but not used [-Wunused-variable]
16 | *global_alpha_size_,
| ^~~~~~~~~~~~~~~~~~
global.h:13:35: warning: 'global_dtimes_' defined but not used [-Wunused-variable]
13 | *global_dtimes_;
| ^~~~~~~~~~~~~~
fam_LLBeta.h: In function 'double fam_LLBeta(double, int*, int*, int*, double*, int, std::vector<std::__cxx11::basic_string<char> >&)':
fam_LLBeta.h:24:17: warning: storing the address of local variable 'beta' in 'global_beta_' [-Wdangling-pointer=]
24 | global_beta_ = β
| ~~~~~~~~~~~~~~^~~~~~~
fam_LLBeta.h:19:26: note: 'beta' declared here
19 | double fam_LLBeta(double beta, int fam_size[], int dt[], int Delta[],
| ~~~~~~~^~~~
global.h:10:35: note: 'global_beta_' declared here
10 | *global_beta_,
| ^~~~~~~~~~~~
fam_LLBeta.h:23:21: warning: storing the address of local variable 'flag' in 'global_2off_flag_' [-Wdangling-pointer=]
23 | global_2off_flag_ = &flag;
| ~~~~~~~~~~~~~~~~~~^~~~~~~
fam_LLBeta.h:22:7: note: 'flag' declared here
22 | int flag = 0;
| ^~~~
global.h:19:35: note: 'global_2off_flag_' declared here
19 | *global_2off_flag_;
| ^~~~~~~~~~~~~~~~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c effScore.cpp -o effScore.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c effScoreFam.cpp -o effScoreFam.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c fminbr.cpp -o fminbr.o
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/bind/mem_fn.hpp:25,
from /data/gannet/ripley/R/test-dev/BH/include/boost/bind/bind.hpp:26,
from /data/gannet/ripley/R/test-dev/BH/include/boost/bind.hpp:29,
from fminbr.h:3,
from fminbr.cpp:52:
/data/gannet/ripley/R/test-dev/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from /usr/local/gcc13/include/c++/13.2.0/memory:78,
from /data/gannet/ripley/R/test-dev/BH/include/boost/config/no_tr1/memory.hpp:21,
from /data/gannet/ripley/R/test-dev/BH/include/boost/get_pointer.hpp:14:
/usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/bind/detail/requires_cxx11.hpp:9,
from /data/gannet/ripley/R/test-dev/BH/include/boost/bind/bind.hpp:24:
/data/gannet/ripley/R/test-dev/BH/include/boost/config/pragma_message.hpp:24:34: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/bind.hpp:36:1: note: in expansion of macro 'BOOST_PRAGMA_MESSAGE'
36 | BOOST_PRAGMA_MESSAGE(
| ^~~~~~~~~~~~~~~~~~~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c grad_NF.cpp -o grad_NF.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c ll.cpp -o ll.o
In file included from effScoreFam.cpp:4:
global.h:13:35: warning: 'global_dtimes_' defined but not used [-Wunused-variable]
13 | *global_dtimes_;
| ^~~~~~~~~~~~~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c logLike_NF.cpp -o logLike_NF.o
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/bind/mem_fn.hpp:25,
from /data/gannet/ripley/R/test-dev/BH/include/boost/bind/bind.hpp:26,
from /data/gannet/ripley/R/test-dev/BH/include/boost/bind.hpp:29,
from fminbr.h:3,
from ll.cpp:15:
/data/gannet/ripley/R/test-dev/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from /usr/local/gcc13/include/c++/13.2.0/memory:78,
from /data/gannet/ripley/R/test-dev/BH/include/boost/config/no_tr1/memory.hpp:21,
from /data/gannet/ripley/R/test-dev/BH/include/boost/get_pointer.hpp:14:
/usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/bind/detail/requires_cxx11.hpp:9,
from /data/gannet/ripley/R/test-dev/BH/include/boost/bind/bind.hpp:24:
/data/gannet/ripley/R/test-dev/BH/include/boost/config/pragma_message.hpp:24:34: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/bind.hpp:36:1: note: in expansion of macro 'BOOST_PRAGMA_MESSAGE'
36 | BOOST_PRAGMA_MESSAGE(
| ^~~~~~~~~~~~~~~~~~~~
In file included from integrand_est.h:9,
from fam_LL.h:11,
from ll.cpp:14:
global.h:18:35: warning: 'global_alpha_index_' defined but not used [-Wunused-variable]
18 | *global_alpha_index_,
| ^~~~~~~~~~~~~~~~~~~
global.h:16:35: warning: 'global_alpha_size_' defined but not used [-Wunused-variable]
16 | *global_alpha_size_,
| ^~~~~~~~~~~~~~~~~~
global.h:13:35: warning: 'global_dtimes_' defined but not used [-Wunused-variable]
13 | *global_dtimes_;
| ^~~~~~~~~~~~~~
fam_LL.h: In function 'double fam_LL(double, int*, int*, int*, double*, int, std::vector<std::__cxx11::basic_string<char> >&)':
fam_LL.h:26:18: warning: storing the address of local variable 'sigma2' in 'global_sigma2_' [-Wdangling-pointer=]
26 | global_sigma2_ = &sigma2;
| ~~~~~~~~~~~~~~~^~~~~~~~~
fam_LL.h:22:22: note: 'sigma2' declared here
22 | double fam_LL(double sigma2, int fam_size[], int dt[], int Delta[], double G[], int m, std::vector<std::string> &f_ind)
| ~~~~~~~^~~~~~
global.h:11:19: note: 'global_sigma2_' declared here
11 | *global_sigma2_,
| ^~~~~~~~~~~~~~
fam_LL.h:25:21: warning: storing the address of local variable 'flag' in 'global_2off_flag_' [-Wdangling-pointer=]
25 | global_2off_flag_ = &flag;
| ~~~~~~~~~~~~~~~~~~^~~~~~~
fam_LL.h:24:7: note: 'flag' declared here
24 | int flag = 0;
| ^~~~
global.h:19:35: note: 'global_2off_flag_' declared here
19 | *global_2off_flag_;
| ^~~~~~~~~~~~~~~~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c varEst.cpp -o varEst.o
In file included from integrand_est.h:9,
from fam_LLVar.h:11,
from varEst.cpp:16:
global.h:18:35: warning: 'global_alpha_index_' defined but not used [-Wunused-variable]
18 | *global_alpha_index_,
| ^~~~~~~~~~~~~~~~~~~
global.h:16:35: warning: 'global_alpha_size_' defined but not used [-Wunused-variable]
16 | *global_alpha_size_,
| ^~~~~~~~~~~~~~~~~~
global.h:13:35: warning: 'global_dtimes_' defined but not used [-Wunused-variable]
13 | *global_dtimes_;
| ^~~~~~~~~~~~~~
fam_LLVar.h: In function 'double fam_LLVar(double, int*, int*, int*, double*, int, std::vector<std::__cxx11::basic_string<char> >&)':
fam_LLVar.h:25:18: warning: storing the address of local variable 'sigma2' in 'global_sigma2_' [-Wdangling-pointer=]
25 | global_sigma2_ = &sigma2;
| ~~~~~~~~~~~~~~~^~~~~~~~~
fam_LLVar.h:19:25: note: 'sigma2' declared here
19 | double fam_LLVar(double sigma2, int fam_size[], int dt[],
| ~~~~~~~^~~~~~
global.h:11:19: note: 'global_sigma2_' declared here
11 | *global_sigma2_,
| ^~~~~~~~~~~~~~
fam_LLVar.h:24:21: warning: storing the address of local variable 'flag' in 'global_2off_flag_' [-Wdangling-pointer=]
24 | global_2off_flag_ = &flag;
| ~~~~~~~~~~~~~~~~~~^~~~~~~
fam_LLVar.h:23:7: note: 'flag' declared here
23 | int flag = 0;
| ^~~~
global.h:19:35: note: 'global_2off_flag_' declared here
19 | *global_2off_flag_;
| ^~~~~~~~~~~~~~~~~
g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o groupedSurv.so Cuhre.o RcppExports.o alphaEst.o betaEst.o effScore.o effScoreFam.o fminbr.o grad_NF.o ll.o logLike_NF.o varEst.o -fopenmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/groupedSurv/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/groupedSurv/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/groupedSurv/src'
installing to /data/gannet/ripley/R/packages/tests-devel/groupedSurv.Rcheck/00LOCK-groupedSurv/00new/groupedSurv/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (groupedSurv)