* installing *source* package ‘OpenABMCovid19’ ... ** package ‘OpenABMCovid19’ successfully unpacked and MD5 sums checked ** using staged installation checking for gsl-config... /usr/bin/gsl-config configure: creating ./config.status config.status: creating src/Makevars ** libs make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-gcc11/OpenABMCovid19/src' /usr/local/gcc11/bin/gcc -I"/data/gannet/ripley/R/R-gcc11/include" -DNDEBUG -I/usr/local/include -I/usr/include -DBUILD_RPKG -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c R_C_interface.c -o R_C_interface.o R_C_interface.c: In function 'R_intervention_vaccinate_age_group': R_C_interface.c:481:8: warning: unused variable 'n_vac' [-Wunused-variable] 481 | long n_vac =intervention_vaccinate_age_group( c_model, fraction_to_vaccinate, | ^~~~~ /usr/local/gcc11/bin/gcc -I"/data/gannet/ripley/R/R-gcc11/include" -DNDEBUG -I/usr/local/include -I/usr/include -DBUILD_RPKG -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c constant.c -o constant.o /usr/local/gcc11/bin/gcc -I"/data/gannet/ripley/R/R-gcc11/include" -DNDEBUG -I/usr/local/include -I/usr/include -DBUILD_RPKG -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c covid19_wrap_R.c -o covid19_wrap_R.o covid19_wrap_R.c: In function '_p_f_p_model_p_struct_individual__void': covid19_wrap_R.c:8689:7: warning: unused variable 'ecode' [-Wunused-variable] 8689 | int ecode = 0; | ^~~~~ covid19_wrap_R.c:8684:15: warning: unused variable 'arg2' [-Wunused-variable] 8684 | individual *arg2 = (individual *) 0 ; | ^~~~ covid19_wrap_R.c:8683:10: warning: unused variable 'arg1' [-Wunused-variable] 8683 | model *arg1 = (model *) 0 ; | ^~~~ covid19_wrap_R.c: In function '_p_f_p_model_p_struct_individual_p_void__void': covid19_wrap_R.c:8775:7: warning: unused variable 'ecode' [-Wunused-variable] 8775 | int ecode = 0; | ^~~~~ covid19_wrap_R.c:8770:9: warning: unused variable 'arg3' [-Wunused-variable] 8770 | void *arg3 = (void *) 0 ; | ^~~~ covid19_wrap_R.c:8769:15: warning: unused variable 'arg2' [-Wunused-variable] 8769 | individual *arg2 = (individual *) 0 ; | ^~~~ covid19_wrap_R.c:8768:10: warning: unused variable 'arg1' [-Wunused-variable] 8768 | model *arg1 = (model *) 0 ; | ^~~~ /usr/local/gcc11/bin/gcc -I"/data/gannet/ripley/R/R-gcc11/include" -DNDEBUG -I/usr/local/include -I/usr/include -DBUILD_RPKG -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c demographics.c -o demographics.o demographics.c: In function 'generate_household_distribution': demographics.c:238:18: warning: variable 'housesize' set but not used [-Wunused-but-set-variable] 238 | int idx, housesize, age; | ^~~~~~~~~ demographics.c:327:11: warning: 'error' may be used uninitialized in this function [-Wmaybe-uninitialized] 327 | if( error > MAX_ALLOWABLE_ERROR ) | ^ /usr/local/gcc11/bin/gcc -I"/data/gannet/ripley/R/R-gcc11/include" -DNDEBUG -I/usr/local/include -I/usr/include -DBUILD_RPKG -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c disease.c -o disease.o /usr/local/gcc11/bin/gcc -I"/data/gannet/ripley/R/R-gcc11/include" -DNDEBUG -I/usr/local/include -I/usr/include -DBUILD_RPKG -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c doctor.c -o doctor.o /usr/local/gcc11/bin/gcc -I"/data/gannet/ripley/R/R-gcc11/include" -DNDEBUG -I/usr/local/include -I/usr/include -DBUILD_RPKG -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c hospital.c -o hospital.o /usr/local/gcc11/bin/gcc -I"/data/gannet/ripley/R/R-gcc11/include" -DNDEBUG -I/usr/local/include -I/usr/include -DBUILD_RPKG -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c individual.c -o individual.o /usr/local/gcc11/bin/gcc -I"/data/gannet/ripley/R/R-gcc11/include" -DNDEBUG -I/usr/local/include -I/usr/include -DBUILD_RPKG -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c input.c -o input.o /usr/local/gcc11/bin/gcc -I"/data/gannet/ripley/R/R-gcc11/include" -DNDEBUG -I/usr/local/include -I/usr/include -DBUILD_RPKG -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c interventions.c -o interventions.o interventions.c: In function 'resolve_quarantine_reasons': interventions.c:1418:28: warning: 'reason' may be used uninitialized in this function [-Wmaybe-uninitialized] 1418 | int n_reasons = 0, reason, i; | ^~~~~~ /usr/local/gcc11/bin/gcc -I"/data/gannet/ripley/R/R-gcc11/include" -DNDEBUG -I/usr/local/include -I/usr/include -DBUILD_RPKG -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c list.c -o list.o list.c: In function 'initialise_node': list.c:18:13: warning: array subscript 'node[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 18 | node->data = data; | ^~ list.c:13:22: note: referencing an object of size 8 allocated by 'malloc' 13 | node* node = malloc(sizeof(node)); | ^~~~~~~~~~~~~~~~~~~~ list.c:19:13: warning: array subscript 'node[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 19 | node->next = NULL; | ^~ list.c:13:22: note: referencing an object of size 8 allocated by 'malloc' 13 | node* node = malloc(sizeof(node)); | ^~~~~~~~~~~~~~~~~~~~ /usr/local/gcc11/bin/gcc -I"/data/gannet/ripley/R/R-gcc11/include" -DNDEBUG -I/usr/local/include -I/usr/include -DBUILD_RPKG -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c model.c -o model.o /usr/local/gcc11/bin/gcc -I"/data/gannet/ripley/R/R-gcc11/include" -DNDEBUG -I/usr/local/include -I/usr/include -DBUILD_RPKG -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c network.c -o network.o model.c: In function 'add_user_network': model.c:1158:31: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1158 | user_network->edges = calloc(n_edges, sizeof(edge)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/gsl/gsl_rng.h:22, from constant.h:11, from params.h:11, from individual.h:16, from model.h:17, from model.c:7: /usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ model.c: In function 'add_user_network_random': model.c:1239:39: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1239 | user_network->opt_pdx_array = calloc( n_indiv, sizeof(long)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/gsl/gsl_rng.h:22, from constant.h:11, from params.h:11, from individual.h:16, from model.h:17, from model.c:7: /usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ model.c:1240:39: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1240 | user_network->opt_int_array = calloc( n_indiv, sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/gsl/gsl_rng.h:22, from constant.h:11, from params.h:11, from individual.h:16, from model.h:17, from model.c:7: /usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ /usr/local/gcc11/bin/gcc -I"/data/gannet/ripley/R/R-gcc11/include" -DNDEBUG -I/usr/local/include -I/usr/include -DBUILD_RPKG -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c nurse.c -o nurse.o /usr/local/gcc11/bin/gcc -I"/data/gannet/ripley/R/R-gcc11/include" -DNDEBUG -I/usr/local/include -I/usr/include -DBUILD_RPKG -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c params.c -o params.o /usr/local/gcc11/bin/gcc -I"/data/gannet/ripley/R/R-gcc11/include" -DNDEBUG -I/usr/local/include -I/usr/include -DBUILD_RPKG -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c strain.c -o strain.o params.c: In function 'set_model_param_test_order_wait_priority': params.c:932:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 932 | if( value == NO_PRIORITY_TEST ) | ^~ params.c:935:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 935 | check_params( model->params ); | ^~~~~~~~~~~~ /usr/local/gcc11/bin/gcc -I"/data/gannet/ripley/R/R-gcc11/include" -DNDEBUG -I/usr/local/include -I/usr/include -DBUILD_RPKG -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utilities.c -o utilities.o /usr/local/gcc11/bin/gcc -I"/data/gannet/ripley/R/R-gcc11/include" -DNDEBUG -I/usr/local/include -I/usr/include -DBUILD_RPKG -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c ward.c -o ward.o /usr/local/gcc11/bin/gcc -shared -L/usr/local/gcc11/lib64 -L/usr/local/lib64 -o OpenABMCovid19.so R_C_interface.o constant.o covid19_wrap_R.o demographics.o disease.o doctor.o hospital.o individual.o input.o interventions.o list.o model.o network.o nurse.o params.o strain.o utilities.o ward.o -lgsl -lgslcblas -lm -lm make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-gcc11/OpenABMCovid19/src' make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-gcc11/OpenABMCovid19/src' make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-gcc11/OpenABMCovid19/src' installing to /data/gannet/ripley/R/packages/tests-gcc11/OpenABMCovid19.Rcheck/00LOCK-OpenABMCovid19/00new/OpenABMCovid19/libs ** R ** inst ** 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 (OpenABMCovid19)