* installing *source* package ‘Ravages’ ...
** package ‘Ravages’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (GCC) 14.2.0’
using C++ compiler: ‘g++-14 (GCC) 14.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/Ravages/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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 GPG.cpp -o GPG.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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 GPG2.cpp -o GPG2.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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 allelecounter.cpp -o allelecounter.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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 allelecounter2.cpp -o allelecounter2.o
allelecounter2.cpp: In function 'Rcpp::List alleles_by_factor(Rcpp::XPtr<matrix4>, Rcpp::LogicalVector, Rcpp::IntegerVector, Rcpp::LogicalVector)':
allelecounter2.cpp:62:26: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
62 | if(which_snps.length() != p_A->nrow)
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
allelecounter2.cpp:83:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
83 | for(size_t i = 0; i < n; i++) {
| ~~^~~
allelecounter2.cpp:92:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
92 | for(size_t i = 0; i < m; i++)
| ~~^~~
allelecounter2.cpp:101:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
101 | for(size_t i = 0; i < nlevels*nb_snps; i++) {
| ~~^~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:24,
from allelecounter.cpp:2:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:24,
from allelecounter2.cpp:2:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TinyThread.h:7,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:6:
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h: In instantiation of 'int RcppParallel::resolveValue(const char*, T, U) [with T = long unsigned int; U = int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:60:28: required from 'void RcppParallel::parallelReduce(std::size_t, std::size_t, Reducer&, std::size_t, int) [with Reducer = allelecounter2; std::size_t = long unsigned int]'
60 | grainSize = resolveValue("RCPP_PARALLEL_GRAIN_SIZE", grainSize, 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
allelecounter2.cpp:96:17: required from here
96 | parallelReduce(0, nb_snps, X);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h:16:23: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare]
16 | if (requestedValue != defaultValue && requestedValue > 0)
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 alleles_by_group.cpp -o alleles_by_group.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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 block_diag.cpp -o block_diag.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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 burden.cpp -o burden.o
alleles_by_group.cpp: In function 'Rcpp::IntegerMatrix alt_alleles_by_factor(Rcpp::XPtr<matrix4>, Rcpp::LogicalVector, Rcpp::IntegerVector, Rcpp::LogicalVector)':
alleles_by_group.cpp:74:26: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
74 | if(which_snps.length() != p_A->nrow)
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
alleles_by_group.cpp:81:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
81 | for(size_t i = 0; i < n; i++) {
| ~~^~~
alleles_by_group.cpp:89:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
89 | for(size_t i = 0; i < m; i++)
| ~~^~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:24,
from alleles_by_group.cpp:2:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TinyThread.h:7,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:6:
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h: In instantiation of 'int RcppParallel::resolveValue(const char*, T, U) [with T = long unsigned int; U = int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:60:28: required from 'void RcppParallel::parallelReduce(std::size_t, std::size_t, Reducer&, std::size_t, int) [with Reducer = ploc; std::size_t = long unsigned int]'
60 | grainSize = resolveValue("RCPP_PARALLEL_GRAIN_SIZE", grainSize, 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alleles_by_group.cpp:95:17: required from here
95 | parallelReduce(0, nb_snps, X);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h:16:23: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare]
16 | if (requestedValue != defaultValue && requestedValue > 0)
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 colsums.cpp -o colsums.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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 count_alternative_alleles.cpp -o count_alternative_alleles.o
count_alternative_alleles.cpp: In function 'Rcpp::IntegerVector count_alternative_alleles(Rcpp::XPtr<matrix4>, Rcpp::LogicalVector, Rcpp::LogicalVector)':
count_alternative_alleles.cpp:73:26: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
73 | if(which_snps.length() != p_A->nrow)
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
count_alternative_alleles.cpp:80:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
80 | for(size_t i = 0; i < n; i++) {
| ~~^~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:24,
from count_alternative_alleles.cpp:2:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TinyThread.h:7,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:6:
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h: In instantiation of 'int RcppParallel::resolveValue(const char*, T, U) [with T = long unsigned int; U = int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:60:28: required from 'void RcppParallel::parallelReduce(std::size_t, std::size_t, Reducer&, std::size_t, int) [with Reducer = caa_p; std::size_t = long unsigned int]'
60 | grainSize = resolveValue("RCPP_PARALLEL_GRAIN_SIZE", grainSize, 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
count_alternative_alleles.cpp:88:17: required from here
88 | parallelReduce(0, nb_snps, X);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h:16:23: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare]
16 | if (requestedValue != defaultValue && requestedValue > 0)
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 itere_combinaisons.cpp -o itere_combinaisons.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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 jaccard.cpp -o jaccard.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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 label_genes.cpp -o label_genes.o
jaccard.cpp: In function 'Rcpp::List Jaccard(Rcpp::XPtr<matrix4>, Rcpp::LogicalVector, Rcpp::LogicalVector)':
jaccard.cpp:157:26: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
157 | if(which_snps.length() != p_A->nrow)
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:24,
from jaccard.cpp:3:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TinyThread.h:7,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:6:
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h: In instantiation of 'int RcppParallel::resolveValue(const char*, T, U) [with T = long unsigned int; U = int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:60:28: required from 'void RcppParallel::parallelReduce(std::size_t, std::size_t, Reducer&, std::size_t, int) [with Reducer = jaccard_para; std::size_t = long unsigned int]'
60 | grainSize = resolveValue("RCPP_PARALLEL_GRAIN_SIZE", grainSize, 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
jaccard.cpp:170:17: required from here
170 | parallelReduce(0, nb_snps, X);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h:16:23: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare]
16 | if (requestedValue != defaultValue && requestedValue > 0)
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 label_multiple_genes.cpp -o label_multiple_genes.o
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/concept/assert.hpp:35,
from /data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:20,
from /data/gannet/ripley/R/test-dev/BH/include/boost/range/concepts.hpp:19,
from /data/gannet/ripley/R/test-dev/BH/include/boost/range/size_type.hpp:20,
from /data/gannet/ripley/R/test-dev/BH/include/boost/range/size.hpp:21,
from /data/gannet/ripley/R/test-dev/BH/include/boost/range/functions.hpp:20,
from /data/gannet/ripley/R/test-dev/BH/include/boost/range/iterator_range_core.hpp:38,
from /data/gannet/ripley/R/test-dev/BH/include/boost/range/iterator_range.hpp:13,
from /data/gannet/ripley/R/test-dev/BH/include/boost/icl/concept/interval_associator.hpp:11,
from /data/gannet/ripley/R/test-dev/BH/include/boost/icl/associative_interval_container.hpp:18,
from /data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_base_set.hpp:24,
from /data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_set.hpp:14,
from /data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_map.hpp:13,
from label_multiple_genes.cpp:3:
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp: In instantiation of 'static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::concepts::usage_requirements<boost::DefaultConstructible<std::pair<int, int> > >]':
/data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:137:5: required from 'struct boost::DefaultConstructible<std::pair<int, int> >'
92 | &::boost::concepts::requirement_<ModelFnPtr>::failed> \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:135:3: required from 'struct boost::DefaultConstructibleConcept<std::pair<int, int> >'
135 | BOOST_concept(DefaultConstructible,(TT))
| ^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of 'template<class Model> boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints<Model, (& Model::constraints)>*) [with Model = boost::DefaultConstructibleConcept<std::pair<int, int> >]'
32 | inline yes has_constraints_(Model*, wrap_constraints<Model,&Model::constraints>* = 0);
| ^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:42:5: required from 'const bool boost::concepts::not_satisfied<boost::DefaultConstructibleConcept<std::pair<int, int> > >::value'
44 | , value = sizeof( detail::has_constraints_((Model*)0) ) == sizeof(detail::yes) );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:45:51: required from 'struct boost::concepts::not_satisfied<boost::DefaultConstructibleConcept<std::pair<int, int> > >'
45 | typedef boost::integral_constant<bool, value> type;
| ^~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp:72:8: required from 'struct boost::concepts::requirement_<void (*)(boost::DefaultConstructibleConcept<std::pair<int, int> >)>'
72 | struct requirement_<void(*)(Model)>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_base_set.hpp:167:9: required from 'boost::icl::interval_base_map<SubType, DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_base_map() [with SubType = boost::icl::interval_map<std::pair<int, int>, std::set<int> >; DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
92 | &::boost::concepts::requirement_<ModelFnPtr>::failed> \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_map.hpp:77:31: required from 'boost::icl::interval_map<DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_map() [with DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
77 | interval_map(): base_type() {}
| ^
label_multiple_genes.cpp:17:40: required from here
17 | icl::interval_map< gene_pos, gene > MAP;
| ^~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp:50:47: warning: 'this' pointer is null [-Wnonnull]
50 | static void failed() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:31:
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/usage.hpp:20:5: note: in a call to non-static member function 'boost::concepts::usage_requirements<Model>::~usage_requirements() [with Model = boost::DefaultConstructible<std::pair<int, int> >]'
20 | ~usage_requirements() { ((Model*)0)->~Model(); }
| ^
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp: In instantiation of 'static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::DefaultConstructibleConcept<std::pair<int, int> >]':
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_base_set.hpp:167:9: required from 'boost::icl::interval_base_map<SubType, DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_base_map() [with SubType = boost::icl::interval_map<std::pair<int, int>, std::set<int> >; DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
92 | &::boost::concepts::requirement_<ModelFnPtr>::failed> \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_map.hpp:77:31: required from 'boost::icl::interval_map<DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_map() [with DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
77 | interval_map(): base_type() {}
| ^
label_multiple_genes.cpp:17:40: required from here
17 | icl::interval_map< gene_pos, gene > MAP;
| ^~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp:50:47: warning: 'this' pointer is null [-Wnonnull]
50 | static void failed() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/mpl/aux_/integral_wrapper.hpp:22,
from /data/gannet/ripley/R/test-dev/BH/include/boost/mpl/int.hpp:20,
from /data/gannet/ripley/R/test-dev/BH/include/boost/mpl/lambda_fwd.hpp:23,
from /data/gannet/ripley/R/test-dev/BH/include/boost/mpl/aux_/na_spec.hpp:18,
from /data/gannet/ripley/R/test-dev/BH/include/boost/mpl/if.hpp:19,
from /data/gannet/ripley/R/test-dev/BH/include/boost/mpl/eval_if.hpp:17,
from /data/gannet/ripley/R/test-dev/BH/include/boost/iterator/iterator_categories.hpp:14,
from /data/gannet/ripley/R/test-dev/BH/include/boost/iterator/advance.hpp:12,
from /data/gannet/ripley/R/test-dev/BH/include/boost/next_prior.hpp:24,
from /data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_base_set.hpp:23:
/data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:135:17: note: in a call to non-static member function 'boost::DefaultConstructibleConcept<std::pair<int, int> >::~DefaultConstructibleConcept()'
135 | BOOST_concept(DefaultConstructible,(TT))
| ^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/preprocessor/cat.hpp:29:34: note: in definition of macro 'BOOST_PP_CAT_I'
29 | # define BOOST_PP_CAT_I(a, b) a ## b
| ^
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/concept_def.hpp:23:12: note: in expansion of macro 'BOOST_PP_CAT'
23 | struct BOOST_PP_CAT(name,Concept) \
| ^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:135:3: note: in expansion of macro 'BOOST_concept'
135 | BOOST_concept(DefaultConstructible,(TT))
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp: In instantiation of 'static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::concepts::usage_requirements<boost::LessThanComparable<std::pair<int, int> > >]':
/data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:243:5: required from 'struct boost::LessThanComparable<std::pair<int, int> >'
92 | &::boost::concepts::requirement_<ModelFnPtr>::failed> \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:241:3: required from 'struct boost::LessThanComparableConcept<std::pair<int, int> >'
241 | BOOST_concept(LessThanComparable,(TT))
| ^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of 'template<class Model> boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints<Model, (& Model::constraints)>*) [with Model = boost::LessThanComparableConcept<std::pair<int, int> >]'
32 | inline yes has_constraints_(Model*, wrap_constraints<Model,&Model::constraints>* = 0);
| ^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:42:5: required from 'const bool boost::concepts::not_satisfied<boost::LessThanComparableConcept<std::pair<int, int> > >::value'
44 | , value = sizeof( detail::has_constraints_((Model*)0) ) == sizeof(detail::yes) );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:45:51: required from 'struct boost::concepts::not_satisfied<boost::LessThanComparableConcept<std::pair<int, int> > >'
45 | typedef boost::integral_constant<bool, value> type;
| ^~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp:72:8: required from 'struct boost::concepts::requirement_<void (*)(boost::LessThanComparableConcept<std::pair<int, int> >)>'
72 | struct requirement_<void(*)(Model)>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_base_set.hpp:168:9: required from 'boost::icl::interval_base_map<SubType, DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_base_map() [with SubType = boost::icl::interval_map<std::pair<int, int>, std::set<int> >; DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
92 | &::boost::concepts::requirement_<ModelFnPtr>::failed> \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_map.hpp:77:31: required from 'boost::icl::interval_map<DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_map() [with DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
77 | interval_map(): base_type() {}
| ^
label_multiple_genes.cpp:17:40: required from here
17 | icl::interval_map< gene_pos, gene > MAP;
| ^~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp:50:47: warning: 'this' pointer is null [-Wnonnull]
50 | static void failed() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/usage.hpp:20:5: note: in a call to non-static member function 'boost::concepts::usage_requirements<Model>::~usage_requirements() [with Model = boost::LessThanComparable<std::pair<int, int> >]'
20 | ~usage_requirements() { ((Model*)0)->~Model(); }
| ^
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp: In instantiation of 'static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::LessThanComparableConcept<std::pair<int, int> >]':
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_base_set.hpp:168:9: required from 'boost::icl::interval_base_map<SubType, DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_base_map() [with SubType = boost::icl::interval_map<std::pair<int, int>, std::set<int> >; DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
92 | &::boost::concepts::requirement_<ModelFnPtr>::failed> \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_map.hpp:77:31: required from 'boost::icl::interval_map<DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_map() [with DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
77 | interval_map(): base_type() {}
| ^
label_multiple_genes.cpp:17:40: required from here
17 | icl::interval_map< gene_pos, gene > MAP;
| ^~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp:50:47: warning: 'this' pointer is null [-Wnonnull]
50 | static void failed() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:241:17: note: in a call to non-static member function 'boost::LessThanComparableConcept<std::pair<int, int> >::~LessThanComparableConcept()'
241 | BOOST_concept(LessThanComparable,(TT))
| ^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/preprocessor/cat.hpp:29:34: note: in definition of macro 'BOOST_PP_CAT_I'
29 | # define BOOST_PP_CAT_I(a, b) a ## b
| ^
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/concept_def.hpp:23:12: note: in expansion of macro 'BOOST_PP_CAT'
23 | struct BOOST_PP_CAT(name,Concept) \
| ^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:241:3: note: in expansion of macro 'BOOST_concept'
241 | BOOST_concept(LessThanComparable,(TT))
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp: In instantiation of 'static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::concepts::usage_requirements<boost::DefaultConstructible<std::set<int> > >]':
/data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:137:5: required from 'struct boost::DefaultConstructible<std::set<int> >'
92 | &::boost::concepts::requirement_<ModelFnPtr>::failed> \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:135:3: required from 'struct boost::DefaultConstructibleConcept<std::set<int> >'
135 | BOOST_concept(DefaultConstructible,(TT))
| ^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of 'template<class Model> boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints<Model, (& Model::constraints)>*) [with Model = boost::DefaultConstructibleConcept<std::set<int> >]'
32 | inline yes has_constraints_(Model*, wrap_constraints<Model,&Model::constraints>* = 0);
| ^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:42:5: required from 'const bool boost::concepts::not_satisfied<boost::DefaultConstructibleConcept<std::set<int> > >::value'
44 | , value = sizeof( detail::has_constraints_((Model*)0) ) == sizeof(detail::yes) );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:45:51: required from 'struct boost::concepts::not_satisfied<boost::DefaultConstructibleConcept<std::set<int> > >'
45 | typedef boost::integral_constant<bool, value> type;
| ^~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp:72:8: required from 'struct boost::concepts::requirement_<void (*)(boost::DefaultConstructibleConcept<std::set<int> >)>'
72 | struct requirement_<void(*)(Model)>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_base_map.hpp:205:9: required from 'boost::icl::interval_base_map<SubType, DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_base_map() [with SubType = boost::icl::interval_map<std::pair<int, int>, std::set<int> >; DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
92 | &::boost::concepts::requirement_<ModelFnPtr>::failed> \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_map.hpp:77:31: required from 'boost::icl::interval_map<DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_map() [with DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
77 | interval_map(): base_type() {}
| ^
label_multiple_genes.cpp:17:40: required from here
17 | icl::interval_map< gene_pos, gene > MAP;
| ^~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp:50:47: warning: 'this' pointer is null [-Wnonnull]
50 | static void failed() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/usage.hpp:20:5: note: in a call to non-static member function 'boost::concepts::usage_requirements<Model>::~usage_requirements() [with Model = boost::DefaultConstructible<std::set<int> >]'
20 | ~usage_requirements() { ((Model*)0)->~Model(); }
| ^
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp: In instantiation of 'static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::DefaultConstructibleConcept<std::set<int> >]':
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_base_map.hpp:205:9: required from 'boost::icl::interval_base_map<SubType, DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_base_map() [with SubType = boost::icl::interval_map<std::pair<int, int>, std::set<int> >; DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
92 | &::boost::concepts::requirement_<ModelFnPtr>::failed> \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_map.hpp:77:31: required from 'boost::icl::interval_map<DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_map() [with DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
77 | interval_map(): base_type() {}
| ^
label_multiple_genes.cpp:17:40: required from here
17 | icl::interval_map< gene_pos, gene > MAP;
| ^~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp:50:47: warning: 'this' pointer is null [-Wnonnull]
50 | static void failed() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:135:17: note: in a call to non-static member function 'boost::DefaultConstructibleConcept<std::set<int> >::~DefaultConstructibleConcept()'
135 | BOOST_concept(DefaultConstructible,(TT))
| ^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/preprocessor/cat.hpp:29:34: note: in definition of macro 'BOOST_PP_CAT_I'
29 | # define BOOST_PP_CAT_I(a, b) a ## b
| ^
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/concept_def.hpp:23:12: note: in expansion of macro 'BOOST_PP_CAT'
23 | struct BOOST_PP_CAT(name,Concept) \
| ^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:135:3: note: in expansion of macro 'BOOST_concept'
135 | BOOST_concept(DefaultConstructible,(TT))
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp: In instantiation of 'static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::concepts::usage_requirements<boost::icl::EqualComparable<std::set<int> > >]':
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/detail/concept_check.hpp:19:9: required from 'struct boost::icl::EqualComparable<std::set<int> >'
92 | &::boost::concepts::requirement_<ModelFnPtr>::failed> \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/detail/concept_check.hpp:17:5: required from 'struct boost::icl::EqualComparableConcept<std::set<int> >'
17 | BOOST_concept(EqualComparable,(Type))
| ^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of 'template<class Model> boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints<Model, (& Model::constraints)>*) [with Model = boost::icl::EqualComparableConcept<std::set<int> >]'
32 | inline yes has_constraints_(Model*, wrap_constraints<Model,&Model::constraints>* = 0);
| ^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:42:5: required from 'const bool boost::concepts::not_satisfied<boost::icl::EqualComparableConcept<std::set<int> > >::value'
44 | , value = sizeof( detail::has_constraints_((Model*)0) ) == sizeof(detail::yes) );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:45:51: required from 'struct boost::concepts::not_satisfied<boost::icl::EqualComparableConcept<std::set<int> > >'
45 | typedef boost::integral_constant<bool, value> type;
| ^~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp:72:8: required from 'struct boost::concepts::requirement_<void (*)(boost::icl::EqualComparableConcept<std::set<int> >)>'
72 | struct requirement_<void(*)(Model)>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_base_map.hpp:206:9: required from 'boost::icl::interval_base_map<SubType, DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_base_map() [with SubType = boost::icl::interval_map<std::pair<int, int>, std::set<int> >; DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
92 | &::boost::concepts::requirement_<ModelFnPtr>::failed> \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_map.hpp:77:31: required from 'boost::icl::interval_map<DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_map() [with DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
77 | interval_map(): base_type() {}
| ^
label_multiple_genes.cpp:17:40: required from here
17 | icl::interval_map< gene_pos, gene > MAP;
| ^~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp:50:47: warning: 'this' pointer is null [-Wnonnull]
50 | static void failed() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/usage.hpp:20:5: note: in a call to non-static member function 'boost::concepts::usage_requirements<Model>::~usage_requirements() [with Model = boost::icl::EqualComparable<std::set<int> >]'
20 | ~usage_requirements() { ((Model*)0)->~Model(); }
| ^
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp: In instantiation of 'static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::icl::EqualComparableConcept<std::set<int> >]':
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_base_map.hpp:206:9: required from 'boost::icl::interval_base_map<SubType, DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_base_map() [with SubType = boost::icl::interval_map<std::pair<int, int>, std::set<int> >; DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
92 | &::boost::concepts::requirement_<ModelFnPtr>::failed> \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_map.hpp:77:31: required from 'boost::icl::interval_map<DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_map() [with DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
77 | interval_map(): base_type() {}
| ^
label_multiple_genes.cpp:17:40: required from here
17 | icl::interval_map< gene_pos, gene > MAP;
| ^~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp:50:47: warning: 'this' pointer is null [-Wnonnull]
50 | static void failed() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/detail/concept_check.hpp:17:19: note: in a call to non-static member function 'boost::icl::EqualComparableConcept<std::set<int> >::~EqualComparableConcept()'
17 | BOOST_concept(EqualComparable,(Type))
| ^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/preprocessor/cat.hpp:29:34: note: in definition of macro 'BOOST_PP_CAT_I'
29 | # define BOOST_PP_CAT_I(a, b) a ## b
| ^
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/concept_def.hpp:23:12: note: in expansion of macro 'BOOST_PP_CAT'
23 | struct BOOST_PP_CAT(name,Concept) \
| ^~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/detail/concept_check.hpp:17:5: note: in expansion of macro 'BOOST_concept'
17 | BOOST_concept(EqualComparable,(Type))
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/usage.hpp: In instantiation of 'boost::concepts::usage_requirements<Model>::~usage_requirements() [with Model = boost::DefaultConstructible<std::pair<int, int> >]':
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp:50:47: required from 'static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::concepts::usage_requirements<boost::DefaultConstructible<std::pair<int, int> > >]'
50 | static void failed() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:137:5: required from 'struct boost::DefaultConstructible<std::pair<int, int> >'
92 | &::boost::concepts::requirement_<ModelFnPtr>::failed> \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:135:3: required from 'struct boost::DefaultConstructibleConcept<std::pair<int, int> >'
135 | BOOST_concept(DefaultConstructible,(TT))
| ^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of 'template<class Model> boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints<Model, (& Model::constraints)>*) [with Model = boost::DefaultConstructibleConcept<std::pair<int, int> >]'
32 | inline yes has_constraints_(Model*, wrap_constraints<Model,&Model::constraints>* = 0);
| ^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:42:5: required from 'const bool boost::concepts::not_satisfied<boost::DefaultConstructibleConcept<std::pair<int, int> > >::value'
44 | , value = sizeof( detail::has_constraints_((Model*)0) ) == sizeof(detail::yes) );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:45:51: required from 'struct boost::concepts::not_satisfied<boost::DefaultConstructibleConcept<std::pair<int, int> > >'
45 | typedef boost::integral_constant<bool, value> type;
| ^~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp:72:8: required from 'struct boost::concepts::requirement_<void (*)(boost::DefaultConstructibleConcept<std::pair<int, int> >)>'
72 | struct requirement_<void(*)(Model)>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_base_set.hpp:167:9: required from 'boost::icl::interval_base_map<SubType, DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_base_map() [with SubType = boost::icl::interval_map<std::pair<int, int>, std::set<int> >; DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
92 | &::boost::concepts::requirement_<ModelFnPtr>::failed> \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_map.hpp:77:31: required from 'boost::icl::interval_map<DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_map() [with DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
77 | interval_map(): base_type() {}
| ^
label_multiple_genes.cpp:17:40: required from here
17 | icl::interval_map< gene_pos, gene > MAP;
| ^~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/usage.hpp:20:48: warning: 'this' pointer is null [-Wnonnull]
20 | ~usage_requirements() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/usage.hpp:37:7: note: in a call to non-static member function 'boost::DefaultConstructible<TT>::~DefaultConstructible() [with TT = std::pair<int, int>]'
37 | ~model()
| ^
/data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:137:5: note: in expansion of macro 'BOOST_CONCEPT_USAGE'
137 | BOOST_CONCEPT_USAGE(DefaultConstructible) {
| ^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/usage.hpp: In instantiation of 'boost::concepts::usage_requirements<Model>::~usage_requirements() [with Model = boost::LessThanComparable<std::pair<int, int> >]':
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp:50:47: required from 'static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::concepts::usage_requirements<boost::LessThanComparable<std::pair<int, int> > >]'
50 | static void failed() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:243:5: required from 'struct boost::LessThanComparable<std::pair<int, int> >'
92 | &::boost::concepts::requirement_<ModelFnPtr>::failed> \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:241:3: required from 'struct boost::LessThanComparableConcept<std::pair<int, int> >'
241 | BOOST_concept(LessThanComparable,(TT))
| ^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of 'template<class Model> boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints<Model, (& Model::constraints)>*) [with Model = boost::LessThanComparableConcept<std::pair<int, int> >]'
32 | inline yes has_constraints_(Model*, wrap_constraints<Model,&Model::constraints>* = 0);
| ^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:42:5: required from 'const bool boost::concepts::not_satisfied<boost::LessThanComparableConcept<std::pair<int, int> > >::value'
44 | , value = sizeof( detail::has_constraints_((Model*)0) ) == sizeof(detail::yes) );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:45:51: required from 'struct boost::concepts::not_satisfied<boost::LessThanComparableConcept<std::pair<int, int> > >'
45 | typedef boost::integral_constant<bool, value> type;
| ^~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp:72:8: required from 'struct boost::concepts::requirement_<void (*)(boost::LessThanComparableConcept<std::pair<int, int> >)>'
72 | struct requirement_<void(*)(Model)>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_base_set.hpp:168:9: required from 'boost::icl::interval_base_map<SubType, DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_base_map() [with SubType = boost::icl::interval_map<std::pair<int, int>, std::set<int> >; DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
92 | &::boost::concepts::requirement_<ModelFnPtr>::failed> \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_map.hpp:77:31: required from 'boost::icl::interval_map<DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_map() [with DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
77 | interval_map(): base_type() {}
| ^
label_multiple_genes.cpp:17:40: required from here
17 | icl::interval_map< gene_pos, gene > MAP;
| ^~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/usage.hpp:20:48: warning: 'this' pointer is null [-Wnonnull]
20 | ~usage_requirements() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/usage.hpp:37:7: note: in a call to non-static member function 'boost::LessThanComparable<TT>::~LessThanComparable() [with TT = std::pair<int, int>]'
37 | ~model()
| ^
/data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:243:5: note: in expansion of macro 'BOOST_CONCEPT_USAGE'
243 | BOOST_CONCEPT_USAGE(LessThanComparable) {
| ^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/usage.hpp: In instantiation of 'boost::concepts::usage_requirements<Model>::~usage_requirements() [with Model = boost::DefaultConstructible<std::set<int> >]':
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp:50:47: required from 'static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::concepts::usage_requirements<boost::DefaultConstructible<std::set<int> > >]'
50 | static void failed() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:137:5: required from 'struct boost::DefaultConstructible<std::set<int> >'
92 | &::boost::concepts::requirement_<ModelFnPtr>::failed> \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:135:3: required from 'struct boost::DefaultConstructibleConcept<std::set<int> >'
135 | BOOST_concept(DefaultConstructible,(TT))
| ^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of 'template<class Model> boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints<Model, (& Model::constraints)>*) [with Model = boost::DefaultConstructibleConcept<std::set<int> >]'
32 | inline yes has_constraints_(Model*, wrap_constraints<Model,&Model::constraints>* = 0);
| ^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:42:5: required from 'const bool boost::concepts::not_satisfied<boost::DefaultConstructibleConcept<std::set<int> > >::value'
44 | , value = sizeof( detail::has_constraints_((Model*)0) ) == sizeof(detail::yes) );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:45:51: required from 'struct boost::concepts::not_satisfied<boost::DefaultConstructibleConcept<std::set<int> > >'
45 | typedef boost::integral_constant<bool, value> type;
| ^~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp:72:8: required from 'struct boost::concepts::requirement_<void (*)(boost::DefaultConstructibleConcept<std::set<int> >)>'
72 | struct requirement_<void(*)(Model)>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_base_map.hpp:205:9: required from 'boost::icl::interval_base_map<SubType, DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_base_map() [with SubType = boost::icl::interval_map<std::pair<int, int>, std::set<int> >; DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
92 | &::boost::concepts::requirement_<ModelFnPtr>::failed> \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_map.hpp:77:31: required from 'boost::icl::interval_map<DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_map() [with DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
77 | interval_map(): base_type() {}
| ^
label_multiple_genes.cpp:17:40: required from here
17 | icl::interval_map< gene_pos, gene > MAP;
| ^~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/usage.hpp:20:48: warning: 'this' pointer is null [-Wnonnull]
20 | ~usage_requirements() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/usage.hpp:37:7: note: in a call to non-static member function 'boost::DefaultConstructible<TT>::~DefaultConstructible() [with TT = std::set<int>]'
37 | ~model()
| ^
/data/gannet/ripley/R/test-dev/BH/include/boost/concept_check.hpp:137:5: note: in expansion of macro 'BOOST_CONCEPT_USAGE'
137 | BOOST_CONCEPT_USAGE(DefaultConstructible) {
| ^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/usage.hpp: In instantiation of 'boost::concepts::usage_requirements<Model>::~usage_requirements() [with Model = boost::icl::EqualComparable<std::set<int> >]':
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp:50:47: required from 'static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::concepts::usage_requirements<boost::icl::EqualComparable<std::set<int> > >]'
50 | static void failed() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/detail/concept_check.hpp:19:9: required from 'struct boost::icl::EqualComparable<std::set<int> >'
92 | &::boost::concepts::requirement_<ModelFnPtr>::failed> \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/detail/concept_check.hpp:17:5: required from 'struct boost::icl::EqualComparableConcept<std::set<int> >'
17 | BOOST_concept(EqualComparable,(Type))
| ^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of 'template<class Model> boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints<Model, (& Model::constraints)>*) [with Model = boost::icl::EqualComparableConcept<std::set<int> >]'
32 | inline yes has_constraints_(Model*, wrap_constraints<Model,&Model::constraints>* = 0);
| ^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:42:5: required from 'const bool boost::concepts::not_satisfied<boost::icl::EqualComparableConcept<std::set<int> > >::value'
44 | , value = sizeof( detail::has_constraints_((Model*)0) ) == sizeof(detail::yes) );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/has_constraints.hpp:45:51: required from 'struct boost::concepts::not_satisfied<boost::icl::EqualComparableConcept<std::set<int> > >'
45 | typedef boost::integral_constant<bool, value> type;
| ^~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/detail/general.hpp:72:8: required from 'struct boost::concepts::requirement_<void (*)(boost::icl::EqualComparableConcept<std::set<int> >)>'
72 | struct requirement_<void(*)(Model)>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_base_map.hpp:206:9: required from 'boost::icl::interval_base_map<SubType, DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_base_map() [with SubType = boost::icl::interval_map<std::pair<int, int>, std::set<int> >; DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
92 | &::boost::concepts::requirement_<ModelFnPtr>::failed> \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/interval_map.hpp:77:31: required from 'boost::icl::interval_map<DomainT, CodomainT, Traits, Compare, Combine, Section, Interval, Alloc>::interval_map() [with DomainT = std::pair<int, int>; CodomainT = std::set<int>; Traits = boost::icl::partial_absorber; Compare = std::less; Combine = boost::icl::inplace_plus; Section = boost::icl::inter_section; Interval = boost::icl::continuous_interval<std::pair<int, int>, std::less>; Alloc = std::allocator]'
77 | interval_map(): base_type() {}
| ^
label_multiple_genes.cpp:17:40: required from here
17 | icl::interval_map< gene_pos, gene > MAP;
| ^~~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/usage.hpp:20:48: warning: 'this' pointer is null [-Wnonnull]
20 | ~usage_requirements() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/data/gannet/ripley/R/test-dev/BH/include/boost/concept/usage.hpp:37:7: note: in a call to non-static member function 'boost::icl::EqualComparable<Type>::~EqualComparable() [with Type = std::set<int>]'
37 | ~model()
| ^
/data/gannet/ripley/R/test-dev/BH/include/boost/icl/detail/concept_check.hpp:19:9: note: in expansion of macro 'BOOST_CONCEPT_USAGE'
19 | BOOST_CONCEPT_USAGE(EqualComparable) {
| ^~~~~~~~~~~~~~~~~~~
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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_stats.cpp -o m4_stats.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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 matrix4.cpp -o matrix4.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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 moments.cpp -o moments.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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 random_bed_matrix.cpp -o random_bed_matrix.o
random_bed_matrix.cpp: In function 'void random_filling_bed_matrix(Rcpp::XPtr<matrix4>, Rcpp::NumericMatrix, Rcpp::NumericVector, int)':
random_bed_matrix.cpp:47:11: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
47 | if(ncol != p_A->ncol || nrow + firstrow > p_A-> nrow) {
| ~~~~~^~~~~~~~~~~~
random_bed_matrix.cpp:47:43: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
47 | if(ncol != p_A->ncol || nrow + firstrow > p_A-> nrow) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~
random_bed_matrix.cpp: In function 'void random_filling_bed_matrix_noHW(Rcpp::XPtr<matrix4>, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericVector, int)':
random_bed_matrix.cpp:79:11: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
79 | if(ncol != p_A->ncol || nrow + firstrow > p_A-> nrow) {
| ~~~~~^~~~~~~~~~~~
random_bed_matrix.cpp:79:43: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
79 | if(ncol != p_A->ncol || nrow + firstrow > p_A-> nrow) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~
gcc-14 -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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 ravages_init.c -o ravages_init.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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 rbm_haplos_freqs.cpp -o rbm_haplos_freqs.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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 rbm_haplos_thresholds.cpp -o rbm_haplos_thresholds.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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 rbm_haplos_thresholds_filling.cpp -o rbm_haplos_thresholds_filling.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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 skat.cpp -o skat.o
In file included from skat.cpp:6:
statistics_class.h: In constructor 'Stats::Stats(Rcpp::XPtr<matrix4>, Rcpp::LogicalVector, Rcpp::IntegerVector, Rcpp::IntegerVector)':
statistics_class.h:70:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
70 | for(size_t i = 0; i < ncol; i++)
| ~~^~~~~~
statistics_class.h:73:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
73 | for(size_t i = 0; i < full_nb_snps; i++)
| ~~^~~~~~~~~~~~~~
statistics_class.h: In member function 'virtual void Stats::update_snps()':
statistics_class.h:112:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
112 | for(size_t i = 0; i < nb_snp_groups; i++)
| ~~^~~~~~~~~~~~~~~
statistics_class.h:117:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
117 | for(size_t i = 0; i < full_nb_snps; i++) {
| ~~^~~~~~~~~~~~~~
statistics_class.h: In member function 'void Stats::keep_one_snp_group(int)':
statistics_class.h:214:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
214 | for(size_t i = 0; i < full_nb_snps; i++)
| ~~^~~~~~~~~~~~~~
statistics_class.h: In member function 'void Stats::set_no_var_some_var()':
statistics_class.h:225:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
225 | for(size_t j = 0; j < true_ncol; j++) {
| ~~^~~~~~~~~~~
statistics_class.h:236:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
236 | for(size_t j = 0; j < ncol; j++) {
| ~~^~~~~~
statistics_class.h: In member function 'Rcpp::List Stats::exact_p_value(Rcpp::IntegerVector)':
statistics_class.h:276:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
276 | for(int i = 0; i < some_var.size(); i++)
| ~~^~~~~~~~~~~~~~~~~
statistics_class.h:280:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
280 | for(int i = 0; i < disp.size(); i++)
| ~~^~~~~~~~~~~~~
skat.cpp: In member function 'virtual void SKAT::extra_update_snps()':
skat.cpp:59:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
59 | for(size_t i = 0; i < full_nb_snps; i++) {
| ~~^~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:24,
from skat.cpp:2:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 skatBootstrap.cpp -o skatBootstrap.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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 skatMoments.cpp -o skatMoments.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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 skatStats.cpp -o skatStats.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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 sum_by_group.cpp -o sum_by_group.o
In file included from skatBootstrap.cpp:6:
statistics_class.h: In constructor 'Stats::Stats(Rcpp::XPtr<matrix4>, Rcpp::LogicalVector, Rcpp::IntegerVector, Rcpp::IntegerVector)':
statistics_class.h:70:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
70 | for(size_t i = 0; i < ncol; i++)
| ~~^~~~~~
statistics_class.h:73:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
73 | for(size_t i = 0; i < full_nb_snps; i++)
| ~~^~~~~~~~~~~~~~
statistics_class.h: In member function 'virtual void Stats::update_snps()':
statistics_class.h:112:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
112 | for(size_t i = 0; i < nb_snp_groups; i++)
| ~~^~~~~~~~~~~~~~~
statistics_class.h:117:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
117 | for(size_t i = 0; i < full_nb_snps; i++) {
| ~~^~~~~~~~~~~~~~
statistics_class.h: In member function 'void Stats::keep_one_snp_group(int)':
statistics_class.h:214:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
214 | for(size_t i = 0; i < full_nb_snps; i++)
| ~~^~~~~~~~~~~~~~
statistics_class.h: In member function 'void Stats::set_no_var_some_var()':
statistics_class.h:225:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
225 | for(size_t j = 0; j < true_ncol; j++) {
| ~~^~~~~~~~~~~
statistics_class.h:236:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
236 | for(size_t j = 0; j < ncol; j++) {
| ~~^~~~~~
statistics_class.h: In member function 'Rcpp::List Stats::exact_p_value(Rcpp::IntegerVector)':
statistics_class.h:276:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
276 | for(int i = 0; i < some_var.size(); i++)
| ~~^~~~~~~~~~~~~~~~~
statistics_class.h:280:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
280 | for(int i = 0; i < disp.size(); i++)
| ~~^~~~~~~~~~~~~
skatBootstrap.cpp: In member function 'virtual void SKATbootstrap::extra_update_snps()':
skatBootstrap.cpp:73:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
73 | for(size_t i = 0; i < full_nb_snps; i++) {
| ~~^~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:24,
from skatBootstrap.cpp:2:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
skatMoments.cpp: In function 'Rcpp::NumericVector skatMoments(Rcpp::XPtr<matrix4>, Rcpp::LogicalVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericVector, Rcpp::IntegerVector, size_t)':
skatMoments.cpp:34:35: warning: comparison of integer expressions of different signedness: 'Rcpp::traits::storage_type<13>::type' {aka 'int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
34 | if(which_snps[i] && region[i] == g+1) {
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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 sum_fst.cpp -o sum_fst.o
In file included from sum_fst.cpp:6:
statistics_class.h: In constructor 'Stats::Stats(Rcpp::XPtr<matrix4>, Rcpp::LogicalVector, Rcpp::IntegerVector, Rcpp::IntegerVector)':
statistics_class.h:70:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
70 | for(size_t i = 0; i < ncol; i++)
| ~~^~~~~~
statistics_class.h:73:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
73 | for(size_t i = 0; i < full_nb_snps; i++)
| ~~^~~~~~~~~~~~~~
statistics_class.h: In member function 'virtual void Stats::update_snps()':
statistics_class.h:112:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
112 | for(size_t i = 0; i < nb_snp_groups; i++)
| ~~^~~~~~~~~~~~~~~
statistics_class.h:117:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
117 | for(size_t i = 0; i < full_nb_snps; i++) {
| ~~^~~~~~~~~~~~~~
statistics_class.h: In member function 'void Stats::keep_one_snp_group(int)':
statistics_class.h:214:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
214 | for(size_t i = 0; i < full_nb_snps; i++)
| ~~^~~~~~~~~~~~~~
statistics_class.h: In member function 'void Stats::set_no_var_some_var()':
statistics_class.h:225:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
225 | for(size_t j = 0; j < true_ncol; j++) {
| ~~^~~~~~~~~~~
statistics_class.h:236:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
236 | for(size_t j = 0; j < ncol; j++) {
| ~~^~~~~~
statistics_class.h: In member function 'Rcpp::List Stats::exact_p_value(Rcpp::IntegerVector)':
statistics_class.h:276:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
276 | for(int i = 0; i < some_var.size(); i++)
| ~~^~~~~~~~~~~~~~~~~
statistics_class.h:280:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
280 | for(int i = 0; i < disp.size(); i++)
| ~~^~~~~~~~~~~~~
sum_fst.cpp: In member function 'virtual void sumfst::compute_stats()':
sum_fst.cpp:28:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
28 | for(size_t i = 0; i < nb_snps; i++) { // boucle sur les SNP
| ~~^~~~~~~~~
sum_fst.cpp:29:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
29 | for(size_t g = 0; g < nb_ind_groups; g++) { // sur les groupes d'invidus
| ~~^~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:24,
from sum_fst.cpp:2:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TinyThread.h:7,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:6:
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h: In instantiation of 'int RcppParallel::resolveValue(const char*, T, U) [with T = long unsigned int; U = int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:60:28: required from 'void RcppParallel::parallelReduce(std::size_t, std::size_t, Reducer&, std::size_t, int) [with Reducer = allelecounter; std::size_t = long unsigned int]'
60 | grainSize = resolveValue("RCPP_PARALLEL_GRAIN_SIZE", grainSize, 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sum_fst.cpp:24:19: required from here
24 | parallelReduce(0, nb_snps, X);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h:16:23: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare]
16 | if (requestedValue != defaultValue && requestedValue > 0)
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 sum_fst1.cpp -o sum_fst1.o
In file included from sum_fst1.cpp:6:
statistics_class.h: In constructor 'Stats::Stats(Rcpp::XPtr<matrix4>, Rcpp::LogicalVector, Rcpp::IntegerVector, Rcpp::IntegerVector)':
statistics_class.h:70:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
70 | for(size_t i = 0; i < ncol; i++)
| ~~^~~~~~
statistics_class.h:73:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
73 | for(size_t i = 0; i < full_nb_snps; i++)
| ~~^~~~~~~~~~~~~~
statistics_class.h: In member function 'virtual void Stats::update_snps()':
statistics_class.h:112:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
112 | for(size_t i = 0; i < nb_snp_groups; i++)
| ~~^~~~~~~~~~~~~~~
statistics_class.h:117:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
117 | for(size_t i = 0; i < full_nb_snps; i++) {
| ~~^~~~~~~~~~~~~~
statistics_class.h: In member function 'void Stats::keep_one_snp_group(int)':
statistics_class.h:214:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
214 | for(size_t i = 0; i < full_nb_snps; i++)
| ~~^~~~~~~~~~~~~~
statistics_class.h: In member function 'void Stats::set_no_var_some_var()':
statistics_class.h:225:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
225 | for(size_t j = 0; j < true_ncol; j++) {
| ~~^~~~~~~~~~~
statistics_class.h:236:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
236 | for(size_t j = 0; j < ncol; j++) {
| ~~^~~~~~
statistics_class.h: In member function 'Rcpp::List Stats::exact_p_value(Rcpp::IntegerVector)':
statistics_class.h:276:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
276 | for(int i = 0; i < some_var.size(); i++)
| ~~^~~~~~~~~~~~~~~~~
statistics_class.h:280:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
280 | for(int i = 0; i < disp.size(); i++)
| ~~^~~~~~~~~~~~~
sum_fst1.cpp: In constructor 'sumfst1::sumfst1(Rcpp::XPtr<matrix4>, Rcpp::LogicalVector, Rcpp::IntegerVector, Rcpp::IntegerVector)':
sum_fst1.cpp:19:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
19 | for(size_t i = 0; i < full_nb_snps; i++) {
| ~~^~~~~~~~~~~~~~
sum_fst1.cpp:21:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
21 | for(size_t j = 0; j < true_ncol; j++) {
| ~~^~~~~~~~~~~
sum_fst1.cpp:23:46: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
23 | for(int ss = 0; ss < 4 && (4*j + ss) < ncol; ss++) {
| ~~~~~~~~~~~^~~~~~
sum_fst1.cpp: In member function 'virtual void sumfst1::extra_update_snps()':
sum_fst1.cpp:39:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare]
39 | for(size_t i = 0; i < full_nb_snps; i++) {
| ~~^~~~~~~~~~~~~~
sum_fst1.cpp: In member function 'virtual void sumfst1::compute_stats()':
sum_fst1.cpp:57:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
57 | for(size_t i = 0; i < nb_snps; i++) { // boucle sur les SNP
| ~~^~~~~~~~~
sum_fst1.cpp:58:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
58 | for(size_t g = 0; g < nb_ind_groups; g++) { // sur les groupes d'invidus
| ~~^~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:24,
from sum_fst1.cpp:2:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TinyThread.h:7,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:6:
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h: In instantiation of 'int RcppParallel::resolveValue(const char*, T, U) [with T = long unsigned int; U = int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:60:28: required from 'void RcppParallel::parallelReduce(std::size_t, std::size_t, Reducer&, std::size_t, int) [with Reducer = allelecounter; std::size_t = long unsigned int]'
60 | grainSize = resolveValue("RCPP_PARALLEL_GRAIN_SIZE", grainSize, 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sum_fst1.cpp:53:19: required from here
53 | parallelReduce(0, nb_snps, X);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h:16:23: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare]
16 | if (requestedValue != defaultValue && requestedValue > 0)
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 weightedGenotypes.cpp -o weightedGenotypes.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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 weighted_left_product.cpp -o weighted_left_product.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/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 weighted_left_product2.cpp -o weighted_left_product2.o
weighted_left_product2.cpp: In function 'Rcpp::NumericMatrix WLP2(const uint8_t**, const double*, size_t, size_t, size_t, const std::vector<double>&, Rcpp::NumericMatrix&)':
weighted_left_product2.cpp:63:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
63 | if(n != v.nrow() || m != we.size()) stop("Dimensions mismatch (WLP2)");
| ~~^~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:24,
from weighted_left_product2.cpp:9:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
weighted_left_product.cpp: In function 'Rcpp::NumericMatrix WLP(const uint8_t**, const double*, size_t, size_t, size_t, const std::vector<double>&, Rcpp::NumericMatrix&)':
weighted_left_product.cpp:71:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
71 | if(n != v.nrow() || m != we.size()) stop("Dimensions mismatch (WLP)");
| ~~^~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:24,
from weighted_left_product.cpp:9:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o Ravages.so GPG.o GPG2.o allelecounter.o allelecounter2.o alleles_by_group.o block_diag.o burden.o colsums.o count_alternative_alleles.o itere_combinaisons.o jaccard.o label_genes.o label_multiple_genes.o m4_stats.o matrix4.o moments.o random_bed_matrix.o ravages_init.o rbm_haplos_freqs.o rbm_haplos_thresholds.o rbm_haplos_thresholds_filling.o skat.o skatBootstrap.o skatMoments.o skatStats.o sum_by_group.o sum_fst.o sum_fst1.o weightedGenotypes.o weighted_left_product.o weighted_left_product2.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/Ravages/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/Ravages/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/Ravages/src'
installing to /data/gannet/ripley/R/packages/tests-devel/Ravages.Rcheck/00LOCK-Ravages/00new/Ravages/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Ravages)