* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘ACEt’ ...
** package ‘ACEt’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-13) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/Rtmppcs5ik/R.INSTALL274af0535cef3a/ACEt/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c AtCtEt.cpp -o AtCtEt.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c AtCtEtp.cpp -o AtCtEtp.o
AtCtEtp.cpp: In function ‘SEXPREC* loglik_AtCtEt_epsp_g_c(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
AtCtEtp.cpp:294:13: warning: unused variable ‘num_a’ [-Wunused-variable]
294 | int num_a = b_a_m.n_cols;
| ^~~~~
AtCtEtp.cpp:295:13: warning: unused variable ‘num_c’ [-Wunused-variable]
295 | int num_c = b_c_m.n_cols;
| ^~~~~
AtCtEtp.cpp:296:13: warning: unused variable ‘num_e’ [-Wunused-variable]
296 | int num_e = b_e_m.n_cols;
| ^~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c AtDtEt.cpp -o AtDtEt.o
AtDtEt.cpp: In function ‘SEXPREC* hessian_AtDtEt_esp_c(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
AtDtEt.cpp:542:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
542 | for(int i=0; i<num_t; i++)
| ^~~
AtDtEt.cpp:549:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
549 | return(Rcpp::wrap(res));
| ^~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c AtEtp.cpp -o AtEtp.o
AtEtp.cpp: In function ‘SEXPREC* loglik_AtEt_epsp_g_c(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
AtEtp.cpp:212:13: warning: unused variable ‘num_a’ [-Wunused-variable]
212 | int num_a = b_a_m.n_cols;
| ^~~~~
AtEtp.cpp:213:13: warning: unused variable ‘num_e’ [-Wunused-variable]
213 | int num_e = b_e_m.n_cols;
| ^~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RInterface.cc -o RInterface.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/arg.hpp:25,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/placeholders.hpp:24,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_concepts.hpp:10,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/range/concepts.hpp:20,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/range/size_type.hpp:20,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/range/size.hpp:21,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/random/hyperexponential_distribution.hpp:29,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/random.hpp:70,
from mcmc.h:6,
from RInterface.cc:1:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mcmc.cc -o mcmc.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/arg.hpp:25,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/placeholders.hpp:24,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_concepts.hpp:10,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/range/concepts.hpp:20,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/range/size_type.hpp:20,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/range/size.hpp:21,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/random/hyperexponential_distribution.hpp:29,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/random.hpp:70,
from mcmc.h:6,
from mcmc.cc:1:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
mcmc.cc: In function ‘void ci_mh_atctet(double*, int*, int*, int*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, double*)’:
mcmc.cc:31:83: warning: typedef ‘gen_type’ locally defined but not used [-Wunused-local-typedefs]
31 | typedef boost::variate_generator<base_generator_type&, distribution_type> gen_type;
| ^~~~~~~~
mcmc.cc:33:84: warning: typedef ‘gen_type3’ locally defined but not used [-Wunused-local-typedefs]
33 | typedef boost::variate_generator<base_generator_type&, distribution_type3> gen_type3;
| ^~~~~~~~~
mcmc.cc: In function ‘void ci_mh_atctet_2(double*, int*, int*, int*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, double*)’:
mcmc.cc:925:36: warning: typedef ‘Mat_i’ locally defined but not used [-Wunused-local-typedefs]
925 | typedef std::vector<Vec_i> Mat_i;
| ^~~~~
mcmc.cc:932:83: warning: typedef ‘gen_type’ locally defined but not used [-Wunused-local-typedefs]
932 | typedef boost::variate_generator<base_generator_type&, distribution_type> gen_type;
| ^~~~~~~~
mcmc.cc:934:84: warning: typedef ‘gen_type3’ locally defined but not used [-Wunused-local-typedefs]
934 | typedef boost::variate_generator<base_generator_type&, distribution_type3> gen_type3;
| ^~~~~~~~~
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c packagename_init.c -o packagename_init.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o ACEt.so AtCtEt.o AtCtEtp.o AtDtEt.o AtEtp.o RInterface.o mcmc.o packagename_init.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmppcs5ik/R.INSTALL274af0535cef3a/ACEt/src'
make[1]: Entering directory '/tmp/Rtmppcs5ik/R.INSTALL274af0535cef3a/ACEt/src'
make[1]: Leaving directory '/tmp/Rtmppcs5ik/R.INSTALL274af0535cef3a/ACEt/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-ACEt/00new/ACEt/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘ACEt’
finding HTML links ... done
ACEt-package html
AtCtEt html
AtCtEtp html
AtDtEt html
acetp_mcmc html
data_ace html
plot_acet html
test_acetp html
** 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 (ACEt)