* installing *source* package ‘hibayes’ ...
** package ‘hibayes’ 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/hibayes/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'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I'/data/gannet/ripley/R/R-devel/library/Matrix/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -DARMA_64BIT_WORD=1 -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 -DR_NO_REMAP -c Bayes.cpp -o Bayes.o
In file included from Bayes.cpp:1:
hibayes.h:13:9: warning: "R_NO_REMAP" redefined
13 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
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'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I'/data/gannet/ripley/R/R-devel/library/Matrix/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -DARMA_64BIT_WORD=1 -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 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.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'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I'/data/gannet/ripley/R/R-devel/library/Matrix/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -DARMA_64BIT_WORD=1 -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 -DR_NO_REMAP -c SBayesD.cpp -o SBayesD.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'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I'/data/gannet/ripley/R/R-devel/library/Matrix/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -DARMA_64BIT_WORD=1 -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 -DR_NO_REMAP -c SBayesS.cpp -o SBayesS.o
In file included from SBayesD.cpp:1:
hibayes.h:13:9: warning: "R_NO_REMAP" redefined
13 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
In file included from SBayesS.cpp:1:
hibayes.h:13:9: warning: "R_NO_REMAP" redefined
13 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
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'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I'/data/gannet/ripley/R/R-devel/library/Matrix/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -DARMA_64BIT_WORD=1 -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 -DR_NO_REMAP -c cg.cpp -o cg.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'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I'/data/gannet/ripley/R/R-devel/library/Matrix/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -DARMA_64BIT_WORD=1 -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 -DR_NO_REMAP -c cutwind.cpp -o cutwind.o
Bayes.cpp: In function 'Rcpp::List makeZ(const Rcpp::CharacterVector&)':
Bayes.cpp:38:22: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
38 | if (value.size() == n){
| ~~~~~~~~~~~~~^~~~
Bayes.cpp:45:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
45 | for (int j = 0; j < value.size(); j++){
| ~~^~~~~~~~~~~~~~
Bayes.cpp: In function 'Rcpp::List Bayes(arma::vec&, arma::mat&, std::string, arma::vec, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<Rcpp::Matrix<16> >, Rcpp::Nullable<arma::Col<double> >, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::SpMat<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<arma::Col<long long unsigned int> >, int, int, bool)':
Bayes.cpp:103:22: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
103 | for(int i = 0; i < Pi.n_elem; i++){
| ~~^~~~~~~~~~~
Bayes.cpp:178:22: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
178 | if(R_.nrow() != X.n_rows) throw Rcpp::exception("Number of individuals does not match for environmental random effects.");
| ~~~~~~~~~~^~~~~~~~~~~
Bayes.cpp:405:26: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
405 | for(int i = 0; i < Pi.n_elem; i++){
| ~~^~~~~~~~~~~
Bayes.cpp:419:30: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
419 | for(int i = 0; i < fold_.n_elem; i++){
| ~~^~~~~~~~~~~~~~
Bayes.cpp:1008:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
1008 | for(int j = 0; j < (Z_levels[i]).size(); j++){
| ~~^~~~~~~~~~~~~~~~~~~~~~
Bayes.cpp:1045:26: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
1045 | for(int i = 0; i < Pi.n_elem; i++){
| ~~^~~~~~~~~~~
Bayes.cpp:1054:22: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
1054 | if(i != (Pi.n_elem - 1)) Rcpp::Rcout << ", ";
| ~~^~~~~~~~~~~~~~~~~~
SBayesS.cpp: In function 'double spsubmatmtp(arma::sp_mat, arma::vec, arma::uvec)':
SBayesS.cpp:8:22: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
8 | for(int i = 0; i < windxi.n_elem; i++){
| ~~^~~~~~~~~~~~~~~
SBayesS.cpp:10:26: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
10 | for(int j = 0; j < windxi.n_elem; j++){
| ~~^~~~~~~~~~~~~~~
SBayesS.cpp: In function 'Rcpp::List SBayesS(arma::mat, arma::sp_mat, std::string, arma::vec, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, int, int, bool)':
SBayesS.cpp:56:22: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
56 | for(int i = 0; i < Pi.n_elem; i++){
| ~~^~~~~~~~~~~
SBayesD.cpp: In function 'Rcpp::List SBayesD(arma::mat, arma::mat, std::string, arma::vec, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, int, int, bool)':
SBayesD.cpp:40:22: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
40 | for(int i = 0; i < Pi.n_elem; i++){
| ~~^~~~~~~~~~~
SBayesS.cpp:225:26: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
225 | for(int i = 0; i < Pi.n_elem; i++){
| ~~^~~~~~~~~~~
SBayesS.cpp:239:30: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
239 | for(int i = 0; i < fold_.n_elem; i++){
| ~~^~~~~~~~~~~~~~
SBayesD.cpp:197:26: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
197 | for(int i = 0; i < Pi.n_elem; i++){
| ~~^~~~~~~~~~~
SBayesD.cpp:211:30: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
211 | for(int i = 0; i < fold_.n_elem; i++){
| ~~^~~~~~~~~~~~~~
SBayesS.cpp:652:26: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
652 | for(int i = 0; i < Pi.n_elem; i++){
| ~~^~~~~~~~~~~
SBayesS.cpp:661:22: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
661 | if(i != (Pi.n_elem - 1)) Rcpp::Rcout << ", ";
| ~~^~~~~~~~~~~~~~~~~~
SBayesD.cpp:582:26: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
582 | for(int i = 0; i < Pi.n_elem; i++){
| ~~^~~~~~~~~~~
SBayesD.cpp:591:22: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
591 | if(i != (Pi.n_elem - 1)) Rcpp::Rcout << ", ";
| ~~^~~~~~~~~~~~~~~~~~
cg.cpp: In function 'Rcpp::List conjgt_spa(Rcpp::NumericMatrix, arma::sp_mat, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >, double, int, bool)':
cg.cpp:15:27: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
15 | if(sumstat.nrow() != ldm.n_rows){
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~
cg.cpp: In function 'Rcpp::List conjgt_den(Rcpp::NumericMatrix, arma::mat, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >, double, int, bool)':
cg.cpp:79:27: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
79 | if(sumstat.nrow() != ldm.n_rows){
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~
cutwind.cpp: In function 'arma::vec cutwind_by_bp(const arma::vec&, const arma::vec&, double)':
cutwind.cpp:21:26: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
21 | for(int i = 0; i < unichr.n_elem; i++){
| ~~^~~~~~~~~~~~~~~
cutwind.cpp: In function 'arma::vec cutwind_by_num(const arma::vec&, const arma::vec&, int)':
cutwind.cpp:45:26: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
45 | for(int i = 0; i < unichr.n_elem; i++){
| ~~^~~~~~~~~~~~~~~
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'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I'/data/gannet/ripley/R/R-devel/library/Matrix/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -DARMA_64BIT_WORD=1 -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 -DR_NO_REMAP -c read_bed.cpp -o read_bed.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'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I'/data/gannet/ripley/R/R-devel/library/Matrix/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -DARMA_64BIT_WORD=1 -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 -DR_NO_REMAP -c rm.cpp -o rm.o
In file included from rm.cpp:1:
hibayes.h:13:9: warning: "R_NO_REMAP" redefined
13 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /data/gannet/ripley/R/test-dev/BH/include/boost/shared_ptr.hpp:17,
from /data/gannet/ripley/R/test-dev/bigmemory/include/bigmemory/BigMatrix.h:10,
from read_bed.cpp:4:
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
In file included from /usr/local/gcc14/include/c++/14.2.0/memory:78,
from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
/usr/local/gcc14/include/c++/14.2.0/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
/usr/local/gcc14/include/c++/14.2.0/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
/usr/local/gcc14/include/c++/14.2.0/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
/usr/local/gcc14/include/c++/14.2.0/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
/usr/local/gcc14/include/c++/14.2.0/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
/usr/local/gcc14/include/c++/14.2.0/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
/usr/local/gcc14/include/c++/14.2.0/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
read_bed.cpp: In instantiation of 'void read_bed(std::string, Rcpp::XPtr<BigMatrix>, long int, double, bool, bool, int) [with T = char; std::string = std::__cxx11::basic_string<char>]':
read_bed.cpp:240:24: required from here
240 | return read_bed<char>(bfile, xpMat, maxLine, NA_CHAR, impt, d, threads);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_bed.cpp:155:40: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
155 | for (size_t j = 0; j < cond; j++) {
| ^~~~
read_bed.cpp:160:54: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'index_type' {aka 'long int'} [-Wsign-compare]
160 | for (x = 0; x < 4 && (c + x) < pMat->nrow(); x++) {
| ~~~~~~~~^~~~~~~~~~~~~~
read_bed.cpp:218:46: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
218 | if(counts[j] > max){
read_bed.cpp:142:16: warning: variable 'n_bytes_read' set but not used [-Wunused-but-set-variable]
142 | size_t n_bytes_read = static_cast<size_t>(fread(buffer, 1, 3, fin));
| ^~~~~~~~~~~~
read_bed.cpp: In instantiation of 'void read_bed(std::string, Rcpp::XPtr<BigMatrix>, long int, double, bool, bool, int) [with T = short int; std::string = std::__cxx11::basic_string<char>]':
read_bed.cpp:242:25: required from here
242 | return read_bed<short>(bfile, xpMat, maxLine, NA_SHORT, impt, d, threads);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_bed.cpp:155:40: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
155 | for (size_t j = 0; j < cond; j++) {
| ^~~~
read_bed.cpp:160:54: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'index_type' {aka 'long int'} [-Wsign-compare]
160 | for (x = 0; x < 4 && (c + x) < pMat->nrow(); x++) {
| ~~~~~~~~^~~~~~~~~~~~~~
read_bed.cpp:218:46: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
218 | if(counts[j] > max){
read_bed.cpp:142:16: warning: variable 'n_bytes_read' set but not used [-Wunused-but-set-variable]
142 | size_t n_bytes_read = static_cast<size_t>(fread(buffer, 1, 3, fin));
| ^~~~~~~~~~~~
read_bed.cpp: In instantiation of 'void read_bed(std::string, Rcpp::XPtr<BigMatrix>, long int, double, bool, bool, int) [with T = int; std::string = std::__cxx11::basic_string<char>]':
read_bed.cpp:244:23: required from here
244 | return read_bed<int>(bfile, xpMat, maxLine, NA_INTEGER, impt, d, threads);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_bed.cpp:155:40: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
155 | for (size_t j = 0; j < cond; j++) {
| ^~~~
read_bed.cpp:160:54: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'index_type' {aka 'long int'} [-Wsign-compare]
160 | for (x = 0; x < 4 && (c + x) < pMat->nrow(); x++) {
| ~~~~~~~~^~~~~~~~~~~~~~
read_bed.cpp:218:46: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
218 | if(counts[j] > max){
read_bed.cpp:142:16: warning: variable 'n_bytes_read' set but not used [-Wunused-but-set-variable]
142 | size_t n_bytes_read = static_cast<size_t>(fread(buffer, 1, 3, fin));
| ^~~~~~~~~~~~
read_bed.cpp: In instantiation of 'void read_bed(std::string, Rcpp::XPtr<BigMatrix>, long int, double, bool, bool, int) [with T = double; std::string = std::__cxx11::basic_string<char>]':
read_bed.cpp:246:26: required from here
246 | return read_bed<double>(bfile, xpMat, maxLine, NA_REAL, impt, d, threads);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_bed.cpp:155:40: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
155 | for (size_t j = 0; j < cond; j++) {
| ^~~~
read_bed.cpp:160:54: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'index_type' {aka 'long int'} [-Wsign-compare]
160 | for (x = 0; x < 4 && (c + x) < pMat->nrow(); x++) {
| ~~~~~~~~^~~~~~~~~~~~~~
read_bed.cpp:218:46: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
218 | if(counts[j] > max){
read_bed.cpp:142:16: warning: variable 'n_bytes_read' set but not used [-Wunused-but-set-variable]
142 | size_t n_bytes_read = static_cast<size_t>(fread(buffer, 1, 3, fin));
| ^~~~~~~~~~~~
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'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I'/data/gannet/ripley/R/R-devel/library/Matrix/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -DARMA_64BIT_WORD=1 -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 -DR_NO_REMAP -c solver.cpp -o solver.o
SBayesD.cpp:483:34: warning: 'nw' may be used uninitialized [-Wmaybe-uninitialized]
483 | for(int w = 0; w < nw; w++){
| ~~^~~~
SBayesD.cpp:174:9: note: 'nw' was declared here
174 | int nw;
| ^~
SBayesD.cpp:518:38: warning: 'NnzSnp' may be used uninitialized [-Wmaybe-uninitialized]
518 | Rcpp::Rcout << NnzSnp << " ";
| ^~~
SBayesD.cpp:61:9: note: 'NnzSnp' was declared here
61 | int NnzSnp, indistflag;
| ^~~~~~
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'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I'/data/gannet/ripley/R/R-devel/library/Matrix/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -DARMA_64BIT_WORD=1 -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 -DR_NO_REMAP -c stats.cpp -o stats.o
SBayesS.cpp:553:34: warning: 'nw' may be used uninitialized [-Wmaybe-uninitialized]
553 | for(int w = 0; w < nw; w++){
| ~~^~~~
SBayesS.cpp:202:9: note: 'nw' was declared here
202 | int nw;
| ^~
SBayesS.cpp:588:38: warning: 'NnzSnp' may be used uninitialized [-Wmaybe-uninitialized]
588 | Rcpp::Rcout << NnzSnp << " ";
| ^~~
SBayesS.cpp:78:9: note: 'NnzSnp' was declared here
78 | int NnzSnp, indistflag;
| ^~~~~~
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'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I'/data/gannet/ripley/R/R-devel/library/Matrix/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -DARMA_64BIT_WORD=1 -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 -DR_NO_REMAP -c tXXmat.cpp -o tXXmat.o
In file included from tXXmat.cpp:1:
hibayes.h:13:9: warning: "R_NO_REMAP" redefined
13 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
rm.cpp: In function 'SEXPREC* make_grm(arma::mat&, double, bool, bool, bool)':
rm.cpp:32:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
32 | for (size_t j = 0; j < n; j++) {
| ~~^~~
rm.cpp:33:44: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
33 | for (size_t i = (j + 1); i < n; i++) {
| ~~^~~
rm.cpp: In function 'Rcpp::List make_ped(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, bool)':
rm.cpp:68:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
68 | for(int i = 0; i < pvec.size(); i++){
| ~~^~~~~~~~~~~~~
rm.cpp:159:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
159 | for (int j = 0; j < id.size(); j++){
| ~~^~~~~~~~~~~
rm.cpp:163:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
163 | for(int i = 0; i < id.size(); i++){
| ~~^~~~~~~~~~~
solver.cpp: In function 'arma::vec PCGv(arma::mat, arma::vec, int, double)':
solver.cpp:6:26: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
6 | for(int i = 0; i < dA.n_elem; i++){
| ~~^~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /data/gannet/ripley/R/test-dev/BH/include/boost/shared_ptr.hpp:17,
from /data/gannet/ripley/R/test-dev/bigmemory/include/bigmemory/BigMatrix.h:10,
from tXXmat.cpp:2:
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
In file included from /usr/local/gcc14/include/c++/14.2.0/memory:78,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:38,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
from hibayes.h:8:
/usr/local/gcc14/include/c++/14.2.0/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
/usr/local/gcc14/include/c++/14.2.0/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
/usr/local/gcc14/include/c++/14.2.0/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
/usr/local/gcc14/include/c++/14.2.0/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
/usr/local/gcc14/include/c++/14.2.0/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
/usr/local/gcc14/include/c++/14.2.0/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
/usr/local/gcc14/include/c++/14.2.0/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
tXXmat.cpp: In instantiation of 'SEXPREC* tXXmat_Chr(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = char; SEXP = SEXPREC*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
tXXmat.cpp:614:26: required from here
614 | return tXXmat_Chr<char>(xpMat, chr, chisq, threads, verbose);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tXXmat.cpp:530:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
530 | for(int cc = 0; cc < unichr.n_elem; cc++){
| ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:537:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
537 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:543:54: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
543 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:568:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
568 | for(int cc = 0; cc < unichr.n_elem; cc++){
| ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:576:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
576 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:583:58: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
583 | for(i = j + 1; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:597:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
597 | for (j = 0; j < chrindx.n_elem; j++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:598:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
598 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp: In instantiation of 'SEXPREC* tXXmat_Chr(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = short int; SEXP = SEXPREC*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
tXXmat.cpp:616:27: required from here
616 | return tXXmat_Chr<short>(xpMat, chr, chisq, threads, verbose);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tXXmat.cpp:530:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
530 | for(int cc = 0; cc < unichr.n_elem; cc++){
| ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:537:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
537 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:543:54: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
543 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:568:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
568 | for(int cc = 0; cc < unichr.n_elem; cc++){
| ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:576:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
576 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:583:58: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
583 | for(i = j + 1; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:597:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
597 | for (j = 0; j < chrindx.n_elem; j++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:598:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
598 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp: In instantiation of 'SEXPREC* tXXmat_Chr(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = int; SEXP = SEXPREC*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
tXXmat.cpp:618:25: required from here
618 | return tXXmat_Chr<int>(xpMat, chr, chisq, threads, verbose);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tXXmat.cpp:530:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
530 | for(int cc = 0; cc < unichr.n_elem; cc++){
| ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:537:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
537 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:543:54: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
543 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:568:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
568 | for(int cc = 0; cc < unichr.n_elem; cc++){
| ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:576:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
576 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:583:58: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
583 | for(i = j + 1; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:597:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
597 | for (j = 0; j < chrindx.n_elem; j++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:598:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
598 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp: In instantiation of 'SEXPREC* tXXmat_Chr(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = float; SEXP = SEXPREC*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
tXXmat.cpp:620:27: required from here
620 | return tXXmat_Chr<float>(xpMat, chr, chisq, threads, verbose);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tXXmat.cpp:530:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
530 | for(int cc = 0; cc < unichr.n_elem; cc++){
| ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:537:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
537 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:543:54: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
543 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:568:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
568 | for(int cc = 0; cc < unichr.n_elem; cc++){
| ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:576:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
576 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:583:58: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
583 | for(i = j + 1; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:597:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
597 | for (j = 0; j < chrindx.n_elem; j++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:598:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
598 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp: In instantiation of 'SEXPREC* tXXmat_Chr(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = double; SEXP = SEXPREC*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
tXXmat.cpp:622:28: required from here
622 | return tXXmat_Chr<double>(xpMat, chr, chisq, threads, verbose);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tXXmat.cpp:530:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
530 | for(int cc = 0; cc < unichr.n_elem; cc++){
| ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:537:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
537 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:543:54: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
543 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:568:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
568 | for(int cc = 0; cc < unichr.n_elem; cc++){
| ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:576:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
576 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:583:58: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
583 | for(i = j + 1; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:597:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
597 | for (j = 0; j < chrindx.n_elem; j++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:598:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
598 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp: In instantiation of 'SEXPREC* tXXmat_Chr_gwas(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, SEXP, Rcpp::NumericVector, Rcpp::LogicalVector, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = char; SEXP = SEXPREC*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]':
tXXmat.cpp:828:31: required from here
828 | return tXXmat_Chr_gwas<char>(xpMat, chr, gwasgeno, gwaschr, refindx, gwasindx, chisq, threads, verbose);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tXXmat.cpp:664:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
664 | for(int cc = 0; cc < unichr.n_elem; cc++){
| ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:671:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
671 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:677:54: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
677 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:709:57: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
709 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:715:62: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
715 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:741:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
741 | for(int cc = 0; cc < unichr.n_elem; cc++){
| ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:749:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
749 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:756:58: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
756 | for(i = j + 1; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:774:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
774 | for (j = 0; j < chrindx.n_elem; j++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:775:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
775 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:787:57: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
787 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:793:62: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
793 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:810:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
810 | for (j = 0; j < chrindx.n_elem; j++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:811:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
811 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp: In instantiation of 'SEXPREC* tXXmat_Chr_gwas(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, SEXP, Rcpp::NumericVector, Rcpp::LogicalVector, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = short int; SEXP = SEXPREC*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]':
tXXmat.cpp:830:32: required from here
830 | return tXXmat_Chr_gwas<short>(xpMat, chr, gwasgeno, gwaschr, refindx, gwasindx, chisq, threads, verbose);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tXXmat.cpp:664:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
664 | for(int cc = 0; cc < unichr.n_elem; cc++){
| ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:671:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
671 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:677:54: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
677 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:709:57: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
709 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:715:62: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
715 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:741:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
741 | for(int cc = 0; cc < unichr.n_elem; cc++){
| ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:749:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
749 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:756:58: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
756 | for(i = j + 1; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:774:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
774 | for (j = 0; j < chrindx.n_elem; j++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:775:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
775 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:787:57: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
787 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:793:62: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
793 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:810:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
810 | for (j = 0; j < chrindx.n_elem; j++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:811:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
811 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp: In instantiation of 'SEXPREC* tXXmat_Chr_gwas(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, SEXP, Rcpp::NumericVector, Rcpp::LogicalVector, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = int; SEXP = SEXPREC*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]':
tXXmat.cpp:832:30: required from here
832 | return tXXmat_Chr_gwas<int>(xpMat, chr, gwasgeno, gwaschr, refindx, gwasindx, chisq, threads, verbose);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tXXmat.cpp:664:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
664 | for(int cc = 0; cc < unichr.n_elem; cc++){
| ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:671:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
671 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:677:54: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
677 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:709:57: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
709 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:715:62: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
715 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:741:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
741 | for(int cc = 0; cc < unichr.n_elem; cc++){
| ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:749:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
749 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:756:58: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
756 | for(i = j + 1; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:774:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
774 | for (j = 0; j < chrindx.n_elem; j++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:775:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
775 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:787:57: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
787 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:793:62: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
793 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:810:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
810 | for (j = 0; j < chrindx.n_elem; j++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:811:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
811 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp: In instantiation of 'SEXPREC* tXXmat_Chr_gwas(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, SEXP, Rcpp::NumericVector, Rcpp::LogicalVector, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = float; SEXP = SEXPREC*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]':
tXXmat.cpp:834:32: required from here
834 | return tXXmat_Chr_gwas<float>(xpMat, chr, gwasgeno, gwaschr, refindx, gwasindx, chisq, threads, verbose);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tXXmat.cpp:664:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
664 | for(int cc = 0; cc < unichr.n_elem; cc++){
| ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:671:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
671 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:677:54: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
677 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:709:57: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
709 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:715:62: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
715 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:741:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
741 | for(int cc = 0; cc < unichr.n_elem; cc++){
| ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:749:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
749 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:756:58: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
756 | for(i = j + 1; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:774:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
774 | for (j = 0; j < chrindx.n_elem; j++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:775:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
775 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:787:57: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
787 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:793:62: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
793 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:810:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
810 | for (j = 0; j < chrindx.n_elem; j++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:811:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
811 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp: In instantiation of 'SEXPREC* tXXmat_Chr_gwas(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, SEXP, Rcpp::NumericVector, Rcpp::LogicalVector, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = double; SEXP = SEXPREC*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]':
tXXmat.cpp:836:33: required from here
836 | return tXXmat_Chr_gwas<double>(xpMat, chr, gwasgeno, gwaschr, refindx, gwasindx, chisq, threads, verbose);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tXXmat.cpp:664:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
664 | for(int cc = 0; cc < unichr.n_elem; cc++){
| ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:671:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
671 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:677:54: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
677 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:709:57: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
709 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:715:62: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
715 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:741:36: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
741 | for(int cc = 0; cc < unichr.n_elem; cc++){
| ~~~^~~~~~~~~~~~~~~
tXXmat.cpp:749:49: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
749 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:756:58: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
756 | for(i = j + 1; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:774:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
774 | for (j = 0; j < chrindx.n_elem; j++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:775:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
775 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:787:57: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
787 | for (j = 0; j < chrindx.n_elem; j++){
| ^~~~~~
tXXmat.cpp:793:62: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
793 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:810:39: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
810 | for (j = 0; j < chrindx.n_elem; j++){
| ~~^~~~~~~~~~~~~~~~
tXXmat.cpp:811:46: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
811 | for(i = j; i < chrindx.n_elem; i++){
| ~~^~~~~~~~~~~~~~~~
stats.cpp: In function 'Rcpp::IntegerVector which_c(Rcpp::NumericVector, double, int)':
stats.cpp:99:9: warning: 'logi' may be used uninitialized [-Wmaybe-uninitialized]
99 | if(logi){
| ^~
stats.cpp:82:10: note: 'logi' was declared here
82 | bool logi;
| ^~~~
Bayes.cpp:837:34: warning: 'nw' may be used uninitialized [-Wmaybe-uninitialized]
837 | for(int w = 0; w < nw; w++){
| ~~^~~~
Bayes.cpp:377:9: note: 'nw' was declared here
377 | int nw;
| ^~
Bayes.cpp:856:33: warning: 'vb' may be used uninitialized [-Wmaybe-uninitialized]
856 | vb_store[count] = vb;
Bayes.cpp:204:16: note: 'vb' was declared here
204 | double va, vb;
| ^~
Bayes.cpp:855:33: warning: 'va' may be used uninitialized [-Wmaybe-uninitialized]
855 | va_store[count] = va;
Bayes.cpp:204:12: note: 'va' was declared here
204 | double va, vb;
| ^~
Bayes.cpp:896:42: warning: 'NnzSnp' may be used uninitialized [-Wmaybe-uninitialized]
896 | Rcpp::Rcout << NnzSnp << " ";
| ^~~
Bayes.cpp:281:9: note: 'NnzSnp' was declared here
281 | int NnzSnp, indistflag;
| ^~~~~~
In file included from /usr/local/gcc14/include/c++/14.2.0/iostream:41,
from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:53,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
from hibayes.h:8:
In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]',
inlined from 'Rcpp::List Bayes(arma::vec&, arma::mat&, std::string, arma::vec, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<Rcpp::Matrix<16> >, Rcpp::Nullable<arma::Col<double> >, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::SpMat<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<arma::Col<long long unsigned int> >, int, int, bool)' at Bayes.cpp:1074:88:
/usr/local/gcc14/include/c++/14.2.0/ostream:229:25: warning: 'vasd' may be used uninitialized [-Wmaybe-uninitialized]
229 | { return _M_insert(__f); }
| ~~~~~~~~~^~~~~
Bayes.cpp: In function 'Rcpp::List Bayes(arma::vec&, arma::mat&, std::string, arma::vec, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<Rcpp::Matrix<16> >, Rcpp::Nullable<arma::Col<double> >, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::SpMat<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<arma::Col<long long unsigned int> >, int, int, bool)':
Bayes.cpp:206:12: note: 'vasd' was declared here
206 | double vasd, vbsd;
| ^~~~
In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]',
inlined from 'Rcpp::List Bayes(arma::vec&, arma::mat&, std::string, arma::vec, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<Rcpp::Matrix<16> >, Rcpp::Nullable<arma::Col<double> >, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::SpMat<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<arma::Col<long long unsigned int> >, int, int, bool)' at Bayes.cpp:1074:150:
/usr/local/gcc14/include/c++/14.2.0/ostream:229:25: warning: 'vbsd' may be used uninitialized [-Wmaybe-uninitialized]
229 | { return _M_insert(__f); }
| ~~~~~~~~~^~~~~
Bayes.cpp: In function 'Rcpp::List Bayes(arma::vec&, arma::mat&, std::string, arma::vec, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<Rcpp::Matrix<16> >, Rcpp::Nullable<arma::Col<double> >, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::SpMat<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<arma::Col<long long unsigned int> >, int, int, bool)':
Bayes.cpp:206:18: note: 'vbsd' was declared here
206 | double vasd, vbsd;
| ^~~~
In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]',
inlined from 'Rcpp::List Bayes(arma::vec&, arma::mat&, std::string, arma::vec, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<Rcpp::Matrix<16> >, Rcpp::Nullable<arma::Col<double> >, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::SpMat<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<arma::Col<long long unsigned int> >, int, int, bool)' at Bayes.cpp:1078:89:
/usr/local/gcc14/include/c++/14.2.0/ostream:229:25: warning: 'vepssd' may be used uninitialized [-Wmaybe-uninitialized]
229 | { return _M_insert(__f); }
| ~~~~~~~~~^~~~~
Bayes.cpp: In function 'Rcpp::List Bayes(arma::vec&, arma::mat&, std::string, arma::vec, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<arma::Mat<double> >, Rcpp::Nullable<Rcpp::Matrix<16> >, Rcpp::Nullable<arma::Col<double> >, int, int, int, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::SpMat<double> >, Rcpp::Nullable<arma::Col<long long unsigned int> >, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<double>, Rcpp::Nullable<arma::Col<long long unsigned int> >, int, int, bool)':
Bayes.cpp:238:12: note: 'vepssd' was declared here
238 | double vepssd;
| ^~~~~~
solver.cpp: In function 'arma::vec CG(T, arma::vec, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >, double, int, bool) [with T = arma::Mat<double>]':
solver.cpp:109:9: warning: 'err' may be used uninitialized [-Wmaybe-uninitialized]
109 | if(err < esp){
| ^~
solver.cpp:87:23: note: 'err' was declared here
87 | double alpha, err, beta;
| ^~~
solver.cpp: In function 'arma::vec CG(T, arma::vec, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >, double, int, bool) [with T = arma::SpMat<double>]':
solver.cpp:109:9: warning: 'err' may be used uninitialized [-Wmaybe-uninitialized]
109 | if(err < esp){
| ^~
solver.cpp:87:23: note: 'err' was declared here
87 | double alpha, err, beta;
| ^~~
tXXmat.cpp: In function 'SEXPREC* tXXmat_Chr_gwas(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, SEXP, Rcpp::NumericVector, Rcpp::LogicalVector, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = float]':
tXXmat.cpp:708:41: warning: 'chisq_' may be used uninitialized [-Wmaybe-uninitialized]
708 | #pragma omp parallel for schedule(dynamic) private(j, p1, m1, sum1, i, p12, p2, m2, sum2, k, r)
| ^~~
tXXmat.cpp:643:52: note: 'chisq_' was declared here
643 | double m1, m2, sum1, sum2, p1, p2, p12, r, chisq_;
| ^~~~~~
tXXmat.cpp: In function 'SEXPREC* tXXmat_Chr_gwas(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, SEXP, Rcpp::NumericVector, Rcpp::LogicalVector, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = double]':
tXXmat.cpp:708:41: warning: 'chisq_' may be used uninitialized [-Wmaybe-uninitialized]
708 | #pragma omp parallel for schedule(dynamic) private(j, p1, m1, sum1, i, p12, p2, m2, sum2, k, r)
| ^~~
tXXmat.cpp:643:52: note: 'chisq_' was declared here
643 | double m1, m2, sum1, sum2, p1, p2, p12, r, chisq_;
| ^~~~~~
tXXmat.cpp: In function 'SEXPREC* tXXmat_Chr_gwas(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, SEXP, Rcpp::NumericVector, Rcpp::LogicalVector, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = char]':
tXXmat.cpp:708:41: warning: 'chisq_' may be used uninitialized [-Wmaybe-uninitialized]
708 | #pragma omp parallel for schedule(dynamic) private(j, p1, m1, sum1, i, p12, p2, m2, sum2, k, r)
| ^~~
tXXmat.cpp:643:52: note: 'chisq_' was declared here
643 | double m1, m2, sum1, sum2, p1, p2, p12, r, chisq_;
| ^~~~~~
tXXmat.cpp: In function 'SEXPREC* tXXmat_Chr_gwas(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, SEXP, Rcpp::NumericVector, Rcpp::LogicalVector, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = short int]':
tXXmat.cpp:708:41: warning: 'chisq_' may be used uninitialized [-Wmaybe-uninitialized]
708 | #pragma omp parallel for schedule(dynamic) private(j, p1, m1, sum1, i, p12, p2, m2, sum2, k, r)
| ^~~
tXXmat.cpp:643:52: note: 'chisq_' was declared here
643 | double m1, m2, sum1, sum2, p1, p2, p12, r, chisq_;
| ^~~~~~
tXXmat.cpp: In function 'SEXPREC* tXXmat_Chr_gwas(Rcpp::XPtr<BigMatrix>, Rcpp::NumericVector, SEXP, Rcpp::NumericVector, Rcpp::LogicalVector, Rcpp::NumericVector, Rcpp::Nullable<double>, int, bool) [with T = int]':
tXXmat.cpp:708:41: warning: 'chisq_' may be used uninitialized [-Wmaybe-uninitialized]
708 | #pragma omp parallel for schedule(dynamic) private(j, p1, m1, sum1, i, p12, p2, m2, sum2, k, r)
| ^~~
tXXmat.cpp:643:52: note: 'chisq_' was declared here
643 | double m1, m2, sum1, sum2, p1, p2, p12, r, chisq_;
| ^~~~~~
g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o hibayes.so Bayes.o RcppExports.o SBayesD.o SBayesS.o cg.o cutwind.o read_bed.o rm.o solver.o stats.o tXXmat.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/hibayes/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/hibayes/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/hibayes/src'
installing to /data/gannet/ripley/R/packages/tests-devel/hibayes.Rcheck/00LOCK-hibayes/00new/hibayes/libs
** R
** 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 (hibayes)