* installing *source* package ‘Phase123’ ... ** package ‘Phase123’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (GCC) 14.2.0’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/Phase123/src' g++-14 -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/RcppArmadillo/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 PHASE123CODE.cpp -o PHASE123CODE.o g++-14 -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/RcppArmadillo/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 PHASE123CODE.cpp: In function 'double Like(arma::vec, arma::vec, arma::vec, arma::vec, double, int)': PHASE123CODE.cpp:130:12: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 130 | for(i=0;i<YE.n_rows;i++){ | ~^~~~~~~~~~ PHASE123CODE.cpp:106:7: warning: unused variable 'm' [-Wunused-variable] 106 | int m=0; | ^ PHASE123CODE.cpp: In function 'double Like2(arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, int)': PHASE123CODE.cpp:212:12: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 212 | for(m=0;m<Y.n_rows;m++){ | ~^~~~~~~~~ PHASE123CODE.cpp:223:15: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 223 | for(m=0; m<Y.n_rows;m++){ | ~^~~~~~~~~ PHASE123CODE.cpp: In function 'double GetMin(arma::vec)': PHASE123CODE.cpp:313:12: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 313 | for(j=1;j<DESIRE.n_rows;j++){ | ~^~~~~~~~~~~~~~ PHASE123CODE.cpp: In function 'int GetDose1(arma::vec)': PHASE123CODE.cpp:403:12: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 403 | for(j=0;j<DESIRE.n_rows;j++){ | ~^~~~~~~~~~~~~~ PHASE123CODE.cpp:464:18: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 464 | if(which1==(cumprob.n_rows-1)){ | ~~~~~~^~~~~~~~~~~~~~~~~~~~ PHASE123CODE.cpp: In function 'Rcpp::List RunAdaptiveEffToxTrial(int, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, int, int, int, int, int, arma::vec, arma::vec)': PHASE123CODE.cpp:867:20: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 867 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:912:16: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 912 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:930:16: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 930 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:949:16: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 949 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:980:20: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 980 | for(j=1;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:1001:20: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 1001 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:1008:20: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 1008 | for(j=1;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:1022:22: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 1022 | for(j=1;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:1233:20: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 1233 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:1278:16: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 1278 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:1297:16: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 1297 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:1318:16: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 1318 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:1340:18: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 1340 | for(j=1;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:1365:18: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 1365 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:625:7: warning: unused variable 'Count' [-Wunused-variable] 625 | int Count=0; | ^~~~~ PHASE123CODE.cpp:635:7: warning: unused variable 'nREP' [-Wunused-variable] 635 | int nREP=0; | ^~~~ PHASE123CODE.cpp:678:10: warning: unused variable 'min1' [-Wunused-variable] 678 | double min1=0; | ^~~~ PHASE123CODE.cpp: In function 'int AssignEffTox(arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, int)': PHASE123CODE.cpp:1728:20: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 1728 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:1773:16: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 1773 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:1791:16: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 1791 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:1810:16: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 1810 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:1840:20: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 1840 | for(j=1;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:1517:7: warning: unused variable 'Count' [-Wunused-variable] 1517 | int Count=0; | ^~~~~ PHASE123CODE.cpp:1527:7: warning: unused variable 'nREP' [-Wunused-variable] 1527 | int nREP=0; | ^~~~ PHASE123CODE.cpp:1550:7: warning: unused variable 'm' [-Wunused-variable] 1550 | int m=0; | ^ PHASE123CODE.cpp:1567:7: warning: variable 'STOPPED' set but not used [-Wunused-but-set-variable] 1567 | int STOPPED=0; | ^~~~~~~ PHASE123CODE.cpp:1568:7: warning: unused variable 'i' [-Wunused-variable] 1568 | int i=0; | ^ PHASE123CODE.cpp:1570:10: warning: unused variable 'min1' [-Wunused-variable] 1570 | double min1=0; | ^~~~ PHASE123CODE.cpp:1574:7: warning: unused variable 'nRep' [-Wunused-variable] 1574 | int nRep=0; | ^~~~ PHASE123CODE.cpp: In function 'int RandomEffTox(arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, int)': PHASE123CODE.cpp:2212:16: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 2212 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:2257:12: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 2257 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:2275:12: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 2275 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:2294:12: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 2294 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:2001:7: warning: unused variable 'Count' [-Wunused-variable] 2001 | int Count=0; | ^~~~~ PHASE123CODE.cpp:2011:7: warning: unused variable 'nREP' [-Wunused-variable] 2011 | int nREP=0; | ^~~~ PHASE123CODE.cpp:2034:7: warning: unused variable 'm' [-Wunused-variable] 2034 | int m=0; | ^ PHASE123CODE.cpp:2051:7: warning: variable 'STOPPED' set but not used [-Wunused-but-set-variable] 2051 | int STOPPED=0; | ^~~~~~~ PHASE123CODE.cpp:2052:7: warning: unused variable 'i' [-Wunused-variable] 2052 | int i=0; | ^ PHASE123CODE.cpp:2054:10: warning: unused variable 'min1' [-Wunused-variable] 2054 | double min1=0; | ^~~~ PHASE123CODE.cpp:2058:7: warning: unused variable 'nRep' [-Wunused-variable] 2058 | int nRep=0; | ^~~~ PHASE123CODE.cpp: In function 'int SampleBirth(arma::vec)': PHASE123CODE.cpp:2408:12: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 2408 | for(m=1;m<cumprob.n_rows;m++){ | ~^~~~~~~~~~~~~~~ PHASE123CODE.cpp:2422:14: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 2422 | for(m=1;m<cumprob.n_rows;m++){ | ~^~~~~~~~~~~~~~~ PHASE123CODE.cpp: In function 'Rcpp::List PieceMCMC(arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, int, arma::mat, arma::mat)': PHASE123CODE.cpp:2887:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 2887 | for(j=(Spot+1);j<(s.n_rows-1);j++){ | ~^~~~~~~~~~~~~ PHASE123CODE.cpp:2894:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 2894 | for(j=(Spot+2);j<(lam.n_rows-1);j++){ | ~^~~~~~~~~~~~~~~ PHASE123CODE.cpp:3017:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 3017 | for(j=Spot;j<(lam.n_rows-1);j++){ | ~^~~~~~~~~~~~~~~ PHASE123CODE.cpp:3029:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 3029 | for(j=Spot; j<(s.n_rows-1);j++){ | ~^~~~~~~~~~~~~ PHASE123CODE.cpp:3149:14: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 3149 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:3410:14: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 3410 | for(j=0;j<sstore.n_cols;j++){ | ~^~~~~~~~~~~~~~ PHASE123CODE.cpp:3414:14: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 3414 | for(j=0;j<lamstore.n_cols;j++){ | ~^~~~~~~~~~~~~~~~ PHASE123CODE.cpp:3418:14: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 3418 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:2492:7: warning: unused variable 'b' [-Wunused-variable] 2492 | int b=0; | ^ PHASE123CODE.cpp:2496:7: warning: unused variable 'B1' [-Wunused-variable] 2496 | int B1=B; | ^~ PHASE123CODE.cpp: In function 'arma::mat EFFTOX(arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, int)': PHASE123CODE.cpp:3675:16: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 3675 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:3707:12: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 3707 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:3718:12: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 3718 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:3740:12: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 3740 | for(j=0;j<Dose.n_rows;j++){ | ~^~~~~~~~~~~~ PHASE123CODE.cpp:3540:7: warning: unused variable 'm' [-Wunused-variable] 3540 | int m=0; | ^ g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o Phase123.so PHASE123CODE.o RcppExports.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -fopenmp make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/Phase123/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/Phase123/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/Phase123/src' installing to /data/gannet/ripley/R/packages/tests-devel/Phase123.Rcheck/00LOCK-Phase123/00new/Phase123/libs ** R ** 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 (Phase123)