* installing *source* package ‘sbrl’ ...
** package ‘sbrl’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc-13
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc-13 accepts -g... yes
checking for gcc-13 option to enable C11 features... none needed
checking how to run the C preprocessor... gcc-13 -E
checking whether the compiler supports GNU C++... yes
checking whether g++-13 -std=gnu++17 accepts -g... yes
checking for g++-13 -std=gnu++17 option to enable C++11 features... none needed
checking for gsl-config... /usr/bin/gsl-config
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for gmp.h... yes
checking for __gmpz_init in -lgmp... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/sbrl/src'
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DGMP -I/usr/local/include -I/usr/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DGMP -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 -I/usr/include -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 rcpp_module.cpp -o rcpp_module.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DGMP -I/usr/local/include -I/usr/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DGMP -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 -I/usr/include -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 rulelib.cpp -o rulelib.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DGMP -I/usr/local/include -I/usr/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DGMP -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 -I/usr/include -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 train.cpp -o train.o
train.cpp: In function 'void propose(Ruleset&, std::vector<Rule>&, std::vector<Rule>&, int, double&, double&, double, int&, double&, const Params&, gsl_rng*, int (*)(double, double, double, double, double&, gsl_rng*))':
train.cpp:150:45: warning: 'change_ndx' may be used uninitialized [-Wmaybe-uninitialized]
150 | new_log_post = compute_log_posterior(rs_new,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
151 | rules, nrules, labels, params, 0, change_ndx, prefix_bound);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
train.cpp:116:13: note: 'change_ndx' was declared here
116 | int change_ndx, ndx1, ndx2;
| ^~~~~~~~~~
In file included from rcpp_module.cpp:11:
rcpp_module.cpp: In function 'Rcpp::List _train(int, int, Rcpp::List, Rcpp::CharacterVector, Rcpp::CharacterVector, Rcpp::StringVector, Rcpp::StringVector, Rcpp::IntegerMatrix, Rcpp::IntegerMatrix)':
mytime.h:51:15: warning: variable '_tmp' set but not used [-Wunused-but-set-variable]
51 | float _tmp; \
| ^~~~
rcpp_module.cpp:68:17: note: in expansion of macro 'REPORT_TIME'
68 | REPORT_TIME("Initialize time", "per rule", tv_end, data.nrules);
| ^~~~~~~~~~~
mytime.h:51:15: warning: variable '_tmp' set but not used [-Wunused-but-set-variable]
51 | float _tmp; \
| ^~~~
rcpp_module.cpp:105:17: note: in expansion of macro 'REPORT_TIME'
105 | REPORT_TIME("Time to train", "", tv_end, 1);
| ^~~~~~~~~~~
rcpp_module.cpp:108:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
108 | for (int i=0; i<pred_model_sbrl.ids.size(); i++)
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
rcpp_module.cpp:111:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
111 | for (int i=0; i<pred_model_sbrl.thetas.size(); i++)
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rulelib.cpp: In function 'void rules_init(const std::string&, std::vector<Rule>&, size_t, size_t, int)':
rulelib.cpp:122:31: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long unsigned int'} and 'int' [-Wsign-compare]
122 | if (nsamples_expected != sample_cnt)
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
rulelib.cpp: In static member function 'static Ruleset Ruleset::ruleset_init(int, const std::vector<int>&, std::vector<Rule>&)':
rulelib.cpp:318:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
318 | for (int i = 0; i < idarray.size(); i++) {
| ~~^~~~~~~~~~~~~~~~
rulelib.cpp: In member function 'int Ruleset::pick_random_rule(int, gsl_rng*) const':
rulelib.cpp:524:35: warning: comparison of integer expressions of different signedness: 'const unsigned int' and 'int' [-Wsign-compare]
524 | if (entry.rule_id == new_rule) {
| ~~~~~~~~~~~~~~^~~~~~~~~~~
rulelib.cpp: In function 'int count_ones(v_entry)':
rulelib.cpp:728:23: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
728 | for (i = 0; i < sizeof(v_entry); i++) {
| ~~^~~~~~~~~~~~~~~~~
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 sbrl.so rcpp_module.o rulelib.o train.o -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -lgsl -lgslcblas -lm -lgmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/sbrl/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/sbrl/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/sbrl/src'
installing to /data/gannet/ripley/R/packages/tests-devel/sbrl.Rcheck/00LOCK-sbrl/00new/sbrl/libs
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (sbrl)