* installing *source* package ‘spBFA’ ... ** package ‘spBFA’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-13 (GCC) 13.2.0’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/spBFA/src' 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/RcppArmadillo/include' -I/usr/local/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 CovarianceFunctions.cpp -o CovarianceFunctions.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/RcppArmadillo/include' -I/usr/local/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 DIAG_Conversion.cpp -o DIAG_Conversion.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/RcppArmadillo/include' -I/usr/local/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 DIAG_GetLogLik.cpp -o DIAG_GetLogLik.o DIAG_GetLogLik.cpp: In function 'arma::colvec GetLogLik(Rcpp::List, Rcpp::List, int, bool)': DIAG_GetLogLik.cpp:71:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 71 | for (arma::uword f = 0; f < O; f++) { | ~~^~~ DIAG_GetLogLik.cpp: In function 'double GetLogLikMean(Rcpp::List, Rcpp::List)': DIAG_GetLogLik.cpp:197:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 197 | for (arma::uword f = 0; f < O; f++) { | ~~^~~ 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/RcppArmadillo/include' -I/usr/local/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 DIAG_SamplePPD.cpp -o DIAG_SamplePPD.o DIAG_SamplePPD.cpp: In function 'arma::mat SamplePPD(Rcpp::List, Rcpp::List, int, bool)': DIAG_SamplePPD.cpp:64:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 64 | for (arma::uword f = 0; f < O; f++) { | ~~^~~ DIAG_SamplePPD.cpp:91:35: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 91 | for (arma::uword t = 0; t < Nu; t++) { | ~~^~~~ DIAG_SamplePPD.cpp:92:37: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 92 | for (arma::uword i = 0; i < M; i++) { | ~~^~~ 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/RcppArmadillo/include' -I/usr/local/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 DistributionFunctions.cpp -o DistributionFunctions.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/RcppArmadillo/include' -I/usr/local/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 MCMC_Conversion.cpp -o MCMC_Conversion.o In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:26, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29, from DistributionFunctions.cpp:2: /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ 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/RcppArmadillo/include' -I/usr/local/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 MCMC_Samplers.cpp -o MCMC_Samplers.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/RcppArmadillo/include' -I/usr/local/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 MCMC_Utilities.cpp -o MCMC_Utilities.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/RcppArmadillo/include' -I/usr/local/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 MCMC_bfa_sp.cpp -o MCMC_bfa_sp.o In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:26, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29, from MCMC_Samplers.cpp:2: /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ MCMC_Utilities.cpp: In function 'arma::colvec StoreSamples(datobj, para)': MCMC_Utilities.cpp:139:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 139 | for (arma::uword o = 0; o < O; o++) { | ~~^~~ MCMC_Utilities.cpp:140:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 140 | for (arma::uword i = 0; i < M; i++) { | ~~^~~ MCMC_Utilities.cpp:142:33: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 142 | for (arma::uword j = 0; j < K; j++) { | ~~^~~ MCMC_Utilities.cpp:148:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 148 | for (arma::uword t = 0; t < Nu; t++) { | ~~^~~~ MCMC_Utilities.cpp:149:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 149 | for (arma::uword j = 0; j < K; j++) { | ~~^~~ MCMC_Utilities.cpp:154:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 154 | for (arma::uword c = 0; c < (O - C); c++) { | ~~^~~~~~~~~ MCMC_Utilities.cpp:155:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 155 | for (arma::uword i = 0; i < M; i++) { | ~~^~~ MCMC_Utilities.cpp:160:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 160 | for (arma::uword i = 0; i < O; i++) { | ~~^~~ MCMC_Utilities.cpp:166:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 166 | for (arma::uword j = 0; j < K; j++) { | ~~^~~ MCMC_Utilities.cpp:170:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 170 | for (arma::uword i = 0; i < K; i++) { | ~~^~~ MCMC_Utilities.cpp:178:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 178 | for (arma::uword o = 0; o < O; o++) { | ~~^~~ MCMC_Utilities.cpp:179:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 179 | for (arma::uword i = 0; i < M; i++) { | ~~^~~ MCMC_Utilities.cpp:181:33: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 181 | for (arma::uword j = 0; j < K; j++) { | ~~^~~ MCMC_Utilities.cpp:189:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 189 | for (arma::uword p = 0; p < P; p++) { | ~~^~~ MCMC_Samplers.cpp: In function 'datobj SampleUpper(datobj, para, dataug)': MCMC_Samplers.cpp:54:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 54 | for (arma::uword i = 0; i < NAbove; i++) { | ~~^~~~~~~~ MCMC_Samplers.cpp: In function 'datobj SampleLower(datobj, para, dataug)': MCMC_Samplers.cpp:89:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 89 | for (arma::uword i = 0; i < NBelow; i++) { | ~~^~~~~~~~ MCMC_Samplers.cpp: In function 'std::pair SampleY(datobj, para, dataug)': MCMC_Samplers.cpp:129:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 129 | for (arma::uword f = 0; f < O; f++) { | ~~^~~ MCMC_Samplers.cpp: In function 'para SampleSigma2(datobj, para, hypara)': MCMC_Samplers.cpp:193:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 193 | for (arma::uword c = 0; c < (O - C); c++) { | ~~^~~~~~~~~ MCMC_Samplers.cpp:199:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 199 | for (arma::uword i = 0; i < M; i++) { | ~~^~~ MCMC_Samplers.cpp: In function 'para SampleBeta(datobj, para, hypara)': MCMC_Samplers.cpp:409:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 409 | for (arma::uword t = 0; t < Nu; t++) { | ~~^~~~ MCMC_Samplers.cpp: In function 'para SampleEta(datobj, para, hypara)': MCMC_Samplers.cpp:463:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 463 | for (arma::uword t = 0; t < Nu; t++) { | ~~^~~~ MCMC_Samplers.cpp: In function 'para SampleDelta(datobj, para, hypara)': MCMC_Samplers.cpp:526:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 526 | for (arma::uword h = 0; h < K; h++) { | ~~^~~ MCMC_Samplers.cpp:538:33: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 538 | for (arma::uword j = h; j < K; j++) { | ~~^~~ MCMC_Samplers.cpp:567:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 567 | for (arma::uword j = 0; j < K; j++) { | ~~^~~ MCMC_Samplers.cpp: In function 'std::pair SampleRho(datobj, para, hypara, metrobj)': MCMC_Samplers.cpp:673:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 673 | for (arma::uword j = 0; j < K; j++) { | ~~^~~ MCMC_Samplers.cpp:680:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 680 | for (arma::uword l = 0; l < UpperL; l++) { | ~~^~~~~~~~ MCMC_Samplers.cpp: In function 'para SampleKappa(datobj, para, hypara)': MCMC_Samplers.cpp:752:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 752 | for (arma::uword j = 0; j < K; j++) { | ~~^~~ MCMC_Samplers.cpp:754:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 754 | for (arma::uword l = 0; l < UpperL; l++) { | ~~^~~~~~~~ MCMC_Samplers.cpp: In function 'para SampleAlpha(datobj, para)': MCMC_Samplers.cpp:817:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 817 | for (arma::uword j = 0; j < K; j++) { | ~~^~~ MCMC_Samplers.cpp:825:33: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 825 | for (arma::uword l = 0; l < UpperL; l++) { | ~~^~~~~~~~ MCMC_Samplers.cpp:883:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 883 | for (arma::uword j = 0; j < K; j++) { | ~~^~~ MCMC_Samplers.cpp:893:33: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 893 | for (arma::uword t = 0; t < Nu; t++) { | ~~^~~~ MCMC_Samplers.cpp:898:35: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 898 | for (arma::uword h = 0; h < (K - 1); h++) LambdaSum += LambdaMinusJ.col(h) * BigPhiMinusJ(h, t); | ~~^~~~~~~~~ MCMC_Samplers.cpp: In function 'para SampleZ(datobj, para)': MCMC_Samplers.cpp:950:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 950 | for (arma::uword j = 0; j < K; j++) { | ~~^~~ MCMC_Samplers.cpp:958:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 958 | for (arma::uword o = 0; o < O; o++) { | ~~^~~ MCMC_Samplers.cpp:961:33: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 961 | for (arma::uword i = 0; i < M; i++) { | ~~^~~ MCMC_Samplers.cpp:968:33: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 968 | for (arma::uword l = 0; l < UpperL; l++) { | ~~^~~~~~~~ MCMC_Samplers.cpp: In function 'para SampleXi(datobj, para)': MCMC_Samplers.cpp:1035:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1035 | for (arma::uword j = 0; j < K; j++) { | ~~^~~ MCMC_Samplers.cpp:1044:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1044 | for (arma::uword o = 0; o < O; o++) { | ~~^~~ MCMC_Samplers.cpp:1049:33: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1049 | for (arma::uword i = 0; i < M; i++) { | ~~^~~ MCMC_Samplers.cpp:1061:35: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1061 | for (arma::uword l = 0; l < UpperL; l++) { | ~~^~~~~~~~ MCMC_Samplers.cpp:1110:43: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1110 | for (arma::uword seq = 0; seq < UpperL; seq++) SeqLStarJ(seq) = seq; | ~~~~^~~~~~~~ MCMC_Samplers.cpp: In function 'para SampleTheta(datobj, para)': MCMC_Samplers.cpp:1171:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1171 | for (arma::uword j = 0; j < K; j++) { | ~~^~~ MCMC_Samplers.cpp:1183:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1183 | for (arma::uword l = 0; l < UpperL; l++) { | ~~^~~~~~~~ MCMC_Samplers.cpp: In function 'para SampleU(datobj, para)': MCMC_Samplers.cpp:1251:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1251 | for (arma::uword j = 0; j < K; j++) { | ~~^~~ MCMC_Samplers.cpp:1253:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1253 | for (arma::uword o = 0; o < O; o++) { | ~~^~~ MCMC_Samplers.cpp:1254:33: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1254 | for (arma::uword i = 0; i < M; i++) { | ~~^~~ MCMC_Samplers.cpp: In function 'para SampleZ(datobj, para)': MCMC_Samplers.cpp:974:22: warning: 'ZOIJL' may be used uninitialized [-Wmaybe-uninitialized] 974 | ZJ(l, Index) = ZOIJL; | ~~~~~~~~~~~~~^~~~~~~ MCMC_Samplers.cpp:971:16: note: 'ZOIJL' was declared here 971 | double ZOIJL; | ^~~~~ MCMC_Samplers.cpp: In function 'para SampleDelta(datobj, para, hypara)': MCMC_Samplers.cpp:581:30: warning: 'tThetaTheta' may be used uninitialized [-Wmaybe-uninitialized] 581 | double Rate = A2 + 0.5 * tThetaTheta; | ~~~~^~~~~~~~~~~~~ MCMC_Samplers.cpp:571:14: note: 'tThetaTheta' was declared here 571 | double tThetaTheta; | ^~~~~~~~~~~ MCMC_Samplers.cpp:547:47: warning: 'tThetaTheta' may be used uninitialized [-Wmaybe-uninitialized] 547 | Resids += arma::as_scalar(tThetaTheta * arma::prod(DeltaMinusH(arma::span(0, j)))); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MCMC_Samplers.cpp:540:16: note: 'tThetaTheta' was declared here 540 | double tThetaTheta; | ^~~~~~~~~~~ MCMC_Samplers.cpp: In function 'para SampleXi(datobj, para)': MCMC_Samplers.cpp:1115:22: warning: 'XiOIJ' may be used uninitialized [-Wmaybe-uninitialized] 1115 | Xi(Index, j) = XiOIJ; | ~~~~~~~~~~~~~^~~~~~~ MCMC_Samplers.cpp:1104:21: note: 'XiOIJ' was declared here 1104 | arma::uword XiOIJ; | ^~~~~ MCMC_Samplers.cpp: In function 'para SampleTheta(datobj, para)': MCMC_Samplers.cpp:1213:19: warning: 'ThetaJL' may be used uninitialized [-Wmaybe-uninitialized] 1213 | Theta(l, j) = ThetaJL; | ~~~~~~~~~~~~^~~~~~~~~ MCMC_Samplers.cpp:1190:14: note: 'ThetaJL' was declared here 1190 | double ThetaJL; | ^~~~~~~ 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/RcppArmadillo/include' -I/usr/local/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 PRED_Conversion.cpp -o PRED_Conversion.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/RcppArmadillo/include' -I/usr/local/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 PRED_EtaKrigging.cpp -o PRED_EtaKrigging.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/RcppArmadillo/include' -I/usr/local/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 PRED_YKrigging.cpp -o PRED_YKrigging.o PRED_EtaKrigging.cpp: In function 'arma::mat EtaKrigging(Rcpp::List, Rcpp::List, int, bool)': PRED_EtaKrigging.cpp:50:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 50 | for (arma::uword s = 0; s < NKeep; s++) { | ~~^~~~~~~ PRED_EtaKrigging.cpp:56:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 56 | for (arma::uword i = 0; i < K; i++) { | ~~^~~ PRED_YKrigging.cpp: In function 'arma::cube YKrigging(Rcpp::List, Rcpp::List, arma::mat, int, bool)': PRED_YKrigging.cpp:48:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 48 | for (arma::uword s = 0; s < NKeep; s++) { | ~~^~~~~~~ PRED_YKrigging.cpp:59:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 59 | for (arma::uword n = 0; n < NNewVisits; n++) { | ~~^~~~~~~~~~~~ PRED_YKrigging.cpp:67:33: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 67 | for (arma::uword f = 0; f < O; f++) { | ~~^~~ PRED_YKrigging.cpp:94:37: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 94 | for (arma::uword i = 0; i < M; i++) PredMat(i, f) = rbinomRcpp(TrialsVec(i), Pi(i)); | ~~^~~ 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/RcppArmadillo/include' -I/usr/local/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 Play.cpp -o Play.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/RcppArmadillo/include' -I/usr/local/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 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/RcppArmadillo/include' -I/usr/local/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 UtilityFunctions.cpp -o UtilityFunctions.o UtilityFunctions.cpp: In function 'arma::colvec GetLStarJ(const arma::mat&, const arma::cube&, int, int, int)': UtilityFunctions.cpp:11:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 11 | for (arma::uword j = 0; j < K; j++) { | ~~^~~ UtilityFunctions.cpp:14:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 14 | for (arma::uword o = 0; o < O; o++) { | ~~^~~ UtilityFunctions.cpp:15:33: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 15 | for (arma::uword i = 0; i < M; i++) { | ~~^~~ UtilityFunctions.cpp: In function 'arma::mat GetLambda(const arma::mat&, const arma::umat&, int, int, int)': UtilityFunctions.cpp:33:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 33 | for (arma::uword o = 0; o < O; o++) { | ~~^~~ UtilityFunctions.cpp:34:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 34 | for (arma::uword i = 0; i < M; i++) { | ~~^~~ UtilityFunctions.cpp:36:33: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 36 | for (arma::uword j = 0; j < K; j++) { | ~~^~~ UtilityFunctions.cpp: In function 'arma::cube GetWeights(const arma::cube&, int, int, int, int)': UtilityFunctions.cpp:54:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 54 | for (arma::uword j = 0; j < K; j++) { | ~~^~~ UtilityFunctions.cpp:55:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 55 | for (arma::uword o = 0; o < O; o++) { | ~~^~~ UtilityFunctions.cpp:56:33: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 56 | for (arma::uword i = 0; i < M; i++) { | ~~^~~ UtilityFunctions.cpp:58:35: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 58 | for (arma::uword l = 0; l < L; l ++) { | ~~^~~ UtilityFunctions.cpp:64:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 64 | for (arma::uword j = 0; j < K; j++) { | ~~^~~ UtilityFunctions.cpp:65:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 65 | for (arma::uword o = 0; o < O; o++) { | ~~^~~ UtilityFunctions.cpp:66:33: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 66 | for (arma::uword i = 0; i < M; i++) { | ~~^~~ UtilityFunctions.cpp:68:35: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 68 | for (arma::uword l = 0; l < L; l ++) { | ~~^~~ UtilityFunctions.cpp: In function 'arma::cube GetlogWeights(const arma::cube&, int, int, int, int)': UtilityFunctions.cpp:87:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 87 | for (arma::uword j = 0; j < K; j++) { | ~~^~~ UtilityFunctions.cpp:88:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 88 | for (arma::uword o = 0; o < O; o++) { | ~~^~~ UtilityFunctions.cpp:89:33: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 89 | for (arma::uword i = 0; i < M; i++) { | ~~^~~ UtilityFunctions.cpp:91:35: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 91 | for (arma::uword l = 0; l < L; l ++) { | ~~^~~ UtilityFunctions.cpp:98:29: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 98 | for (arma::uword j = 0; j < K; j++) { | ~~^~~ UtilityFunctions.cpp:99:31: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 99 | for (arma::uword o = 0; o < O; o++) { | ~~^~~ UtilityFunctions.cpp:100:33: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 100 | for (arma::uword i = 0; i < M; i++) { | ~~^~~ UtilityFunctions.cpp:102:35: warning: comparison of integer expressions of different signedness: 'arma::uword' {aka 'unsigned int'} and 'int' [-Wsign-compare] 102 | for (arma::uword l = 0; l < L; l ++) { | ~~^~~ 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 spBFA.so CovarianceFunctions.o DIAG_Conversion.o DIAG_GetLogLik.o DIAG_SamplePPD.o DistributionFunctions.o MCMC_Conversion.o MCMC_Samplers.o MCMC_Utilities.o MCMC_bfa_sp.o PRED_Conversion.o PRED_EtaKrigging.o PRED_YKrigging.o Play.o RcppExports.o UtilityFunctions.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/spBFA/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/spBFA/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/spBFA/src' installing to /data/gannet/ripley/R/packages/tests-devel/spBFA.Rcheck/00LOCK-spBFA/00new/spBFA/libs ** R ** data *** moving datasets to lazyload DB ** 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 (spBFA)