* installing *source* package ‘kgrams’ ...
** package ‘kgrams’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (GCC) 14.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/kgrams/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/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c DictionaryR.cpp -o DictionaryR.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/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c Smoothing.cpp -o Smoothing.o
Smoothing.cpp: In function 'int main()':
Smoothing.cpp:701:16: warning: unused variable 'sum' [-Wunused-variable]
701 | double sum = prob_a + prob_b + prob_eos + prob_unk;
| ^~~
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/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c SmoothingR.cpp -o SmoothingR.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/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c UtilitiesR.cpp -o UtilitiesR.o
In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:46,
from kgramFreqsR.h:4,
from SmoothingR.h:9,
from SmoothingR.cpp:1:
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = Smoother]':
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/module/class.h:38:35: required from 'class Rcpp::class_<Smoother>'
38 | typedef Rcpp::XPtr<Class> XP ;
| ^~
SmoothingR.cpp:108:39: required from here
108 | class_<Smoother>("___Smoother")
| ^
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'Smoother' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
31 | delete obj;
| ^~~~~~~~~~
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = SBOSmoother]':
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/module/class.h:38:35: required from 'class Rcpp::class_<SBOSmoother>'
38 | typedef Rcpp::XPtr<Class> XP ;
| ^~
SmoothingR.cpp:112:45: required from here
112 | class_<SBOSmoother>("___SBOSmoother")
| ^
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'SBOSmoother' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
31 | delete obj;
| ^~~~~~~~~~
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = AddkSmoother]':
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/module/class.h:38:35: required from 'class Rcpp::class_<AddkSmoother>'
38 | typedef Rcpp::XPtr<Class> XP ;
| ^~
SmoothingR.cpp:116:47: required from here
116 | class_<AddkSmoother>("___AddkSmoother")
| ^
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'AddkSmoother' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
31 | delete obj;
| ^~~~~~~~~~
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = MLSmoother]':
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/module/class.h:38:35: required from 'class Rcpp::class_<MLSmoother>'
38 | typedef Rcpp::XPtr<Class> XP ;
| ^~
SmoothingR.cpp:120:43: required from here
120 | class_<MLSmoother>("___MLSmoother")
| ^
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'MLSmoother' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
31 | delete obj;
| ^~~~~~~~~~
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = KNSmoother]':
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/module/class.h:38:35: required from 'class Rcpp::class_<KNSmoother>'
38 | typedef Rcpp::XPtr<Class> XP ;
| ^~
SmoothingR.cpp:123:43: required from here
123 | class_<KNSmoother>("___KNSmoother")
| ^
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'KNSmoother' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
31 | delete obj;
| ^~~~~~~~~~
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = mKNSmoother]':
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/module/class.h:38:35: required from 'class Rcpp::class_<mKNSmoother>'
38 | typedef Rcpp::XPtr<Class> XP ;
| ^~
SmoothingR.cpp:127:45: required from here
127 | class_<mKNSmoother>("___mKNSmoother")
| ^
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'mKNSmoother' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
31 | delete obj;
| ^~~~~~~~~~
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = AbsSmoother]':
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/module/class.h:38:35: required from 'class Rcpp::class_<AbsSmoother>'
38 | typedef Rcpp::XPtr<Class> XP ;
| ^~
SmoothingR.cpp:133:45: required from here
133 | class_<AbsSmoother>("___AbsSmoother")
| ^
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'AbsSmoother' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
31 | delete obj;
| ^~~~~~~~~~
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = WBSmoother]':
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/module/class.h:38:35: required from 'class Rcpp::class_<WBSmoother>'
38 | typedef Rcpp::XPtr<Class> XP ;
| ^~
SmoothingR.cpp:137:43: required from here
137 | class_<WBSmoother>("___WBSmoother")
| ^
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'WBSmoother' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
31 | delete obj;
| ^~~~~~~~~~
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = SBOSmootherR]':
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/module/class.h:38:35: required from 'class Rcpp::class_<SBOSmootherR>'
38 | typedef Rcpp::XPtr<Class> XP ;
| ^~
SmoothingR.cpp:140:43: required from here
140 | class_<SBOSmootherR>("SBOSmoother")
| ^
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'SBOSmootherR' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
31 | delete obj;
| ^~~~~~~~~~
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = MLSmootherR]':
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/module/class.h:38:35: required from 'class Rcpp::class_<MLSmootherR>'
38 | typedef Rcpp::XPtr<Class> XP ;
| ^~
SmoothingR.cpp:148:41: required from here
148 | class_<MLSmootherR>("MLSmoother")
| ^
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'MLSmootherR' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
31 | delete obj;
| ^~~~~~~~~~
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = AddkSmootherR]':
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/module/class.h:38:35: required from 'class Rcpp::class_<AddkSmootherR>'
38 | typedef Rcpp::XPtr<Class> XP ;
| ^~
SmoothingR.cpp:156:45: required from here
156 | class_<AddkSmootherR>("AddkSmoother")
| ^
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'AddkSmootherR' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
31 | delete obj;
| ^~~~~~~~~~
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = KNSmootherR]':
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/module/class.h:38:35: required from 'class Rcpp::class_<KNSmootherR>'
38 | typedef Rcpp::XPtr<Class> XP ;
| ^~
SmoothingR.cpp:164:41: required from here
164 | class_<KNSmootherR>("KNSmoother")
| ^
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'KNSmootherR' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
31 | delete obj;
| ^~~~~~~~~~
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = mKNSmootherR]':
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/module/class.h:38:35: required from 'class Rcpp::class_<mKNSmootherR>'
38 | typedef Rcpp::XPtr<Class> XP ;
| ^~
SmoothingR.cpp:172:43: required from here
172 | class_<mKNSmootherR>("mKNSmoother")
| ^
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'mKNSmootherR' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
31 | delete obj;
| ^~~~~~~~~~
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = AbsSmootherR]':
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/module/class.h:38:35: required from 'class Rcpp::class_<AbsSmootherR>'
38 | typedef Rcpp::XPtr<Class> XP ;
| ^~
SmoothingR.cpp:180:43: required from here
180 | class_<AbsSmootherR>("AbsSmoother")
| ^
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'AbsSmootherR' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
31 | delete obj;
| ^~~~~~~~~~
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = WBSmootherR]':
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/module/class.h:38:35: required from 'class Rcpp::class_<WBSmootherR>'
38 | typedef Rcpp::XPtr<Class> XP ;
| ^~
SmoothingR.cpp:188:41: required from here
188 | class_<WBSmootherR>("WBSmoother")
| ^
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'WBSmootherR' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
31 | delete obj;
| ^~~~~~~~~~
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/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c kgramFreqs.cpp -o kgramFreqs.o
kgramFreqs.cpp: In member function 'CircularBuffer<std::__cxx11::basic_string<char> > kgramFreqs::generate_padding()':
kgramFreqs.cpp:60:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
60 | for (int k = 0; k < N_; ++k) {
| ~~^~~~
kgramFreqs.cpp:62:38: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
62 | for (size_t j = 0; j < k; ++j) {
| ~~^~~
kgramFreqs.cpp: In member function 'void kgramFreqs::add_BOS_counts(size_t)':
kgramFreqs.cpp:73:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
73 | for (int k = 1; k < N_; ++k) {
| ~~^~~~
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/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c kgramFreqsR.cpp -o kgramFreqsR.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/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c special_tokensR.cpp -o special_tokensR.o
g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o kgrams.so DictionaryR.o RcppExports.o Smoothing.o SmoothingR.o UtilitiesR.o kgramFreqs.o kgramFreqsR.o special_tokensR.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/kgrams/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/kgrams/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/kgrams/src'
installing to /data/gannet/ripley/R/packages/tests-devel/kgrams.Rcheck/00LOCK-kgrams/00new/kgrams/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 (kgrams)