* installing *source* package ‘eFCM’ ...
** this is package ‘eFCM’ version ‘1.0’
** package ‘eFCM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
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/eFCM/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 -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
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
from RcppExports.cpp:4:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
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 -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 functions.cpp -o functions.o
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
from functions.cpp:1:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
functions.cpp: In function ‘arma::vec qF1(const arma::vec&, const arma::vec&)’:
functions.cpp:102:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
102 | for(int i = 0; i < u.size(); i+=1){
| ~~^~~~~~~~~~
functions.cpp: In function ‘arma::vec dF1(const arma::vec&, const arma::vec&, const bool&)’:
functions.cpp:389:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
389 | for(int i =0; i<z.size();i+=1){
| ~^~~~~~~~~
functions.cpp: In function ‘double dFI(const arma::vec&, const arma::uvec&, const arma::mat&, const arma::vec&, const double&, const bool&)’:
functions.cpp:420:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
420 | if(k == sigma.n_cols){
| ~~^~~~~~~~~~~~~~~
functions.cpp:450:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
450 | for (int i = 0; i < sigma_I.n_rows; i += 1) {
| ~~^~~~~~~~~~~~~~~~
functions.cpp:451:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
451 | for (int j = 0; j < sigma_I.n_cols; j+= 1) {
| ~~^~~~~~~~~~~~~~~~
functions.cpp: In function ‘double log_partialCn(const arma::vec&, const arma::mat&, const arma::vec&, const arma::mat&, const double&)’:
functions.cpp:485:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
485 | for(int i = 0; i < data_u.n_rows; i += 1){
| ~~^~~~~~~~~~~~~~~
functions.cpp: In function ‘double Log_Lik_Non(const arma::vec&, const arma::mat&, const arma::mat&, const double&)’:
functions.cpp:515:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
515 | for(int i = 0; i < data_u.n_rows; i += 1){
| ~~^~~~~~~~~~~~~~~
functions.cpp:516:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
516 | for(int j = 0; j < data_u.n_cols;j += 1){
| ~~^~~~~~~~~~~~~~~
functions.cpp:528:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
528 | for(int i = 0; i < z.n_rows; i += 1){
| ~~^~~~~~~~~~
functions.cpp:530:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
530 | for(int j = 0; j < z.n_cols; j += 1){
| ~~^~~~~~~~~~
functions.cpp: In function ‘double model_likelihood(const arma::vec&, const arma::mat&, const arma::mat&, const double&, const double&, const bool&)’:
functions.cpp:555:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
555 | for(int i = 0; i < data_u.n_cols; i += 1){
| ~~^~~~~~~~~~~~~~~
functions.cpp:578:25: warning: comparison of integer expressions of different signedness: ‘arma::uword’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
578 | if(bvec.size() == n1){
| ~~~~~~~~~~~~^~~~~
functions.cpp: In function ‘Rcpp::List fit_initial(arma::mat, arma::mat, const arma::uvec&)’:
functions.cpp:646:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
646 | for(int i = 0; i < data.n_rows; i += 1){
| ~~^~~~~~~~~~~~~
functions.cpp:656:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
656 | for(int i = 0; i < data.n_cols; i += 1){
| ~~^~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o eFCM.so RcppExports.o functions.o -fopenmp -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/eFCM/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/eFCM/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/eFCM/src'
installing to /data/gannet/ripley/R/packages/tests-devel/eFCM.Rcheck/00LOCK-eFCM/00new/eFCM/libs
** R
** data
** 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 (eFCM)