* installing *source* package ‘growfunctions’ ... ** this is package ‘growfunctions’ version ‘0.16’ ** package ‘growfunctions’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’ using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/growfunctions/src' g++ -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 dpmix.cpp -o dpmix.o dpmix.cpp: In function ‘SEXPREC* IGMRFDPMIX(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: dpmix.cpp:150:18: warning: ‘bool arma::is_finite(const Base<typename T1::elem_type, T1>&) [with T1 = Mat<double>; typename T1::elem_type = double]’ is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations] 150 | if( is_finite(ksi) ) /* grab number of predictors, R. */ | ~~~~~~~~~^~~~~ In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:518, 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:32, from growfunctions.h:11, from dpmix.cpp:1: /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:181:1: note: declared here 181 | is_finite(const Base<typename T1::elem_type,T1>& X) | ^~~~~~~~~ dpmix.cpp:159:18: warning: ‘bool arma::is_finite(const Base<typename T1::elem_type, T1>&) [with T1 = Mat<double>; typename T1::elem_type = double]’ is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations] 159 | if( is_finite(ksi) ) | ~~~~~~~~~^~~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:181:1: note: declared here 181 | is_finite(const Base<typename T1::elem_type,T1>& X) | ^~~~~~~~~ dpmix.cpp:252:23: warning: ‘bool arma::is_finite(const Base<typename T1::elem_type, T1>&) [with T1 = Mat<double>; typename T1::elem_type = double]’ is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations] 252 | if( !is_finite(ksi) ) /* no dependent PPM */ | ~~~~~~~~~^~~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:181:1: note: declared here 181 | is_finite(const Base<typename T1::elem_type,T1>& X) | ^~~~~~~~~ g++ -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 dpmix_count.cpp -o dpmix_count.o g++ -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 dpmix_moves.cpp -o dpmix_moves.o dpmix_count.cpp: In function ‘SEXPREC* IGMRFDPMIXCOUNT(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: dpmix_count.cpp:157:18: warning: ‘bool arma::is_finite(const Base<typename T1::elem_type, T1>&) [with T1 = Mat<double>; typename T1::elem_type = double]’ is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations] 157 | if( is_finite(ksi) ) /* grab number of predictors, R. */ | ~~~~~~~~~^~~~~ In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:518, 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:32, from growfunctions.h:11, from dpmix_count.cpp:1: /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:181:1: note: declared here 181 | is_finite(const Base<typename T1::elem_type,T1>& X) | ^~~~~~~~~ dpmix_count.cpp:166:18: warning: ‘bool arma::is_finite(const Base<typename T1::elem_type, T1>&) [with T1 = Mat<double>; typename T1::elem_type = double]’ is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations] 166 | if( is_finite(ksi) ) | ~~~~~~~~~^~~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:181:1: note: declared here 181 | is_finite(const Base<typename T1::elem_type,T1>& X) | ^~~~~~~~~ dpmix_count.cpp:293:23: warning: ‘bool arma::is_finite(const Base<typename T1::elem_type, T1>&) [with T1 = Mat<double>; typename T1::elem_type = double]’ is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations] 293 | if( !is_finite(ksi) ) /* no dependent PPM */ | ~~~~~~~~~^~~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:181:1: note: declared here 181 | is_finite(const Base<typename T1::elem_type,T1>& X) | ^~~~~~~~~ g++ -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 gen_bb.cpp -o gen_bb.o g++ -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 gp.cpp -o gp.o g++ -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 gpbfix.cpp -o gpbfix.o g++ -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 gpdpbmix.cpp -o gpdpbmix.o g++ -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 gpdpmix.cpp -o gpdpmix.o g++ -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 gpdpmix_moves.cpp -o gpdpmix_moves.o g++ -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 gpfix.cpp -o gpfix.o gcc -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 -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c growfunctions_init.c -o growfunctions_init.o g++ -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 lsqcluster_cpp.cpp -o lsqcluster_cpp.o g++ -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 sppmcarmix_moves.cpp -o sppmcarmix_moves.o g++ -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 utility.cpp -o utility.o g++ -std=gnu++17 -shared -L/usr/local/lib64 -o growfunctions.so dpmix.o dpmix_count.o dpmix_moves.o gen_bb.o gp.o gpbfix.o gpdpbmix.o gpdpmix.o gpdpmix_moves.o gpfix.o growfunctions_init.o lsqcluster_cpp.o sppmcarmix_moves.o utility.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/growfunctions/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/growfunctions/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/growfunctions/src' installing to /data/gannet/ripley/R/packages/tests-devel/growfunctions.Rcheck/00LOCK-growfunctions/00new/growfunctions/libs ** R ** data ** 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 (growfunctions)