* installing *source* package ‘fastLink’ ...
** this is package ‘fastLink’ version ‘0.6.1’
** package ‘fastLink’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
using C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/fastLink/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/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
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/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 fastLink_init.c -o fastLink_init.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/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 helpers.cpp -o helpers.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/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 m_func_cpp.cpp -o m_func_cpp.o
m_func_cpp.cpp: In function ‘arma::mat indexing(std::vector<arma::Col<double> >, int, int, int, int)’:
m_func_cpp.cpp:42:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   42 |       for(i = 0; i < temp0.n_elem; i++){
      |                  ~~^~~~~~~~~~~~~~
m_func_cpp.cpp:43:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   43 |         for(j = 0; j < temp1.n_elem; j++){
      |                    ~~^~~~~~~~~~~~~~
m_func_cpp.cpp: In function ‘std::vector<Eigen::SparseMatrix<double, 0, int> > unpack_matches(std::vector<std::vector<arma::Mat<double> > >, arma::vec, bool)’:
m_func_cpp.cpp:98:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<arma::Mat<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   98 |     for(j = 0; j < feature_adj.size(); j++){
      |                ~~^~~~~~~~~~~~~~~~~~~~
m_func_cpp.cpp:116:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<arma::Mat<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  116 |     for(j = 0; j < feature_adj.size(); j++){
      |                ~~^~~~~~~~~~~~~~~~~~~~
m_func_cpp.cpp:119:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  119 |         for(k = 0; k < adj_store.n_rows; k++){
      |                    ~~^~~~~~~~~~~~~~~~~~
m_func_cpp.cpp: In function ‘arma::vec getNotIn(arma::vec, arma::vec)’:
m_func_cpp.cpp:141:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  141 |   for(i = 0; i < vec1.n_elem; i++){
      |              ~~^~~~~~~~~~~~~
m_func_cpp.cpp:143:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  143 |     for(j = 0; j < vec2.n_elem; j++){
      |                ~~^~~~~~~~~~~~~
m_func_cpp.cpp: In function ‘std::vector<Eigen::SparseMatrix<double, 0, int> > create_sparse_na(std::vector<std::vector<arma::Col<double> > >, arma::vec)’:
m_func_cpp.cpp:172:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<arma::Col<double> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  172 |   for(i = 0; i < nas.size(); i++){
      |              ~~^~~~~~~~~~~~
m_func_cpp.cpp:187:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
  187 |     for(j = 0; j < nas_a.size(); j++){
      |                ~~^~~~~~~~~~~~~~
m_func_cpp.cpp:192:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
  192 |     for(j = 0; j < nas_b.size(); j++){
      |                ~~^~~~~~~~~~~~~~
m_func_cpp.cpp:193:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
  193 |       for(k = 0; k < nobs_a_notnull_inb.size(); k++){
      |                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
m_func_cpp.cpp: In function ‘std::vector<arma::Col<double> > m_func(std::vector<std::vector<arma::Mat<double> > >, std::vector<std::vector<arma::Mat<double> > >, std::vector<std::vector<arma::Col<double> > >, arma::vec, arma::vec, arma::vec, bool)’:
m_func_cpp.cpp:232:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Eigen::SparseMatrix<double, 0, int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  232 |   for(i = 0; i < matches_up.size(); i++){
      |              ~~^~~~~~~~~~~~~~~~~~~
m_func_cpp.cpp:255:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  255 |     for(i = 0; i < nz_unique_counts.n_elem; i++){
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~
m_func_cpp.cpp: In function ‘std::vector<std::vector<arma::Col<double> > > m_func_par(std::vector<std::vector<std::vector<arma::Col<double> > > >, std::vector<std::vector<std::vector<arma::Col<double> > > >, std::vector<std::vector<arma::Col<double> > >, arma::vec, arma::vec, arma::vec, arma::vec, arma::mat, arma::vec, bool, int)’:
m_func_cpp.cpp:333:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  333 |   for(int i = 0; i < ind.n_rows; i++){
      |                  ~~^~~~~~~~~~~~
m_func_cpp.cpp:341:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::vector<arma::Col<double> > > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  341 |     for(int j = 0; j < temp.size(); j++){
      |                    ~~^~~~~~~~~~~~~
m_func_cpp.cpp:349:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<arma::Col<double> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  349 |       for(k = 0; k < temp_feature.size(); k++){
      |                  ~~^~~~~~~~~~~~~~~~~~~~~
m_func_cpp.cpp:355:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<arma::Col<double> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  355 |       for(k = 0; k < ptemp_feature.size(); k++){
      |                  ~~^~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o fastLink.so RcppExports.o fastLink_init.o helpers.o m_func_cpp.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/fastLink/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/fastLink/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/fastLink/src'
installing to /data/gannet/ripley/R/packages/tests-devel/fastLink.Rcheck/00LOCK-fastLink/00new/fastLink/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (fastLink)