* installing *source* package ‘tidysq’ ...
** this is package ‘tidysq’ version ‘1.2.3’
** package ‘tidysq’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/tidysq/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c apply_R_function.cpp -o apply_R_function.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c bite.cpp -o bite.o
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq.h:5,
from RcppExports.cpp:4:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq/Rcpp-import.h:3,
from apply_R_function.cpp:1:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h: In instantiation of ‘VECTOR_OUT tidysq::sqapply(const VECTOR_IN&, ops::OperationVectorToVector<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>&) [with VECTOR_IN = Sq<RCPP_IT>; ELEMENT_IN = Sequence<RCPP_IT>; VECTOR_OUT = Rcpp::Vector<19>; ELEMENT_OUT = SEXPREC*]’:
../inst/include/tidysq/sqapply.h:23:71: required from ‘VECTOR_OUT tidysq::sqapply(const VECTOR_IN&, ops::OperationVectorToVector<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>&&) [with VECTOR_IN = Sq<RCPP_IT>; ELEMENT_IN = Sequence<RCPP_IT>; VECTOR_OUT = Rcpp::Vector<19>; ELEMENT_OUT = SEXPREC*]’
23 | return sqapply<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>(vector_in, operation);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
../inst/include/tidysq/ops/apply_R_function.h:51:23: required from ‘Rcpp::List tidysq::apply_R_function(const Sq<INTERNAL_IN>&, const Rcpp::Function&) [with INTERNAL_IN = RCPP_IT; PROTO_TMP = STRING_PT; Rcpp::List = Rcpp::Vector<19>; Rcpp::Function = Rcpp::Function_Impl<Rcpp::PreserveStorage>]’
51 | return sqapply(sq, ops::OperationApplyRFunction<INTERNAL_IN, PROTO_TMP>(sq.alphabet(), function));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
apply_R_function.cpp:12:52: required from here
12 | return apply_R_function<RCPP_IT, STRING_PT>(import_sq_from_R(x, NA_letter), fun);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../inst/include/tidysq/sqapply.h:13:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘tidysq::LenSq’ {aka ‘long int’} [-Wsign-compare]
13 | for (u_LenSq i = 0; i < vector_in.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq/Rcpp-import.h:3,
from bite.cpp:3:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
In file included from ../inst/include/tidysq/ops/bite.h:5,
from bite.cpp:1:
../inst/include/tidysq/sqapply.h: In instantiation of ‘VECTOR_OUT tidysq::sqapply(const VECTOR_IN&, ops::OperationVectorToVector<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>&) [with VECTOR_IN = Sq<RCPP_IT>; ELEMENT_IN = Sequence<RCPP_IT>; VECTOR_OUT = Sq<RCPP_IT>; ELEMENT_OUT = Sequence<RCPP_IT>]’:
../inst/include/tidysq/ops/bite.h:71:27: required from ‘tidysq::util::ResultWrapper<tidysq::Sq<INTERNAL_OUT> > tidysq::bite(const Sq<INTERNAL_IN>&, const std::vector<long int>&) [with INTERNAL_IN = RCPP_IT; INTERNAL_OUT = RCPP_IT]’
71 | auto ret = sqapply(sq, op);
| ~~~~~~~^~~~~~~~
bite.cpp:17:30: required from here
17 | bite<RCPP_IT>(import_sq_from_R(x, NA_letter), Rcpp::as<std::vector<LenSq>>(cpp_indices));
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../inst/include/tidysq/sqapply.h:13:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘tidysq::LenSq’ {aka ‘long int’} [-Wsign-compare]
13 | for (u_LenSq i = 0; i < vector_in.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c collapse.cpp -o collapse.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c complement.cpp -o complement.o
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq/Rcpp-import.h:3,
from collapse.cpp:1:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c find_invalid_letters.cpp -o find_invalid_letters.o
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq/Rcpp-import.h:3,
from complement.cpp:4:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
In file included from ../inst/include/tidysq/ops/complement.h:4,
from complement.cpp:3:
../inst/include/tidysq/sqapply.h: In instantiation of ‘VECTOR_OUT tidysq::sqapply(const VECTOR_IN&, ops::OperationVectorToVector<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>&) [with VECTOR_IN = Sq<RCPP_IT>; ELEMENT_IN = Sequence<RCPP_IT>; VECTOR_OUT = Sq<RCPP_IT>; ELEMENT_OUT = Sequence<RCPP_IT>]’:
../inst/include/tidysq/sqapply.h:23:71: required from ‘VECTOR_OUT tidysq::sqapply(const VECTOR_IN&, ops::OperationVectorToVector<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>&&) [with VECTOR_IN = Sq<RCPP_IT>; ELEMENT_IN = Sequence<RCPP_IT>; VECTOR_OUT = Sq<RCPP_IT>; ELEMENT_OUT = Sequence<RCPP_IT>]’
23 | return sqapply<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>(vector_in, operation);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
../inst/include/tidysq/ops/complement.h:79:23: required from ‘tidysq::Sq<INTERNAL_OUT> tidysq::complement(const Sq<INTERNAL_IN>&) [with INTERNAL_IN = RCPP_IT; INTERNAL_OUT = RCPP_IT]’
79 | return sqapply(sq, ops::OperationComplement<INTERNAL_IN, INTERNAL_OUT>(sq.alphabet().alphabet_size(), sq.type()));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
complement.cpp:12:43: required from here
12 | return export_to_R(complement<RCPP_IT>(import_sq_from_R(x, NA_letter)));
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../inst/include/tidysq/sqapply.h:13:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘tidysq::LenSq’ {aka ‘long int’} [-Wsign-compare]
13 | for (u_LenSq i = 0; i < vector_in.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq/Rcpp-import.h:3,
from find_invalid_letters.cpp:2:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
In file included from ../inst/include/tidysq/ops/find_invalid_letters.h:4,
from find_invalid_letters.cpp:1:
../inst/include/tidysq/sqapply.h: In instantiation of ‘VECTOR_OUT tidysq::sqapply(const VECTOR_IN&, ops::OperationVectorToVector<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>&) [with VECTOR_IN = Sq<RCPP_IT>; ELEMENT_IN = Sequence<RCPP_IT>; VECTOR_OUT = std::vector<std::vector<std::__cxx11::basic_string<char> > >; ELEMENT_OUT = std::vector<std::__cxx11::basic_string<char> >]’:
../inst/include/tidysq/sqapply.h:23:71: required from ‘VECTOR_OUT tidysq::sqapply(const VECTOR_IN&, ops::OperationVectorToVector<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>&&) [with VECTOR_IN = Sq<RCPP_IT>; ELEMENT_IN = Sequence<RCPP_IT>; VECTOR_OUT = std::vector<std::vector<std::__cxx11::basic_string<char> > >; ELEMENT_OUT = std::vector<std::__cxx11::basic_string<char> >]’
23 | return sqapply<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>(vector_in, operation);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
../inst/include/tidysq/ops/find_invalid_letters.h:72:23: required from ‘std::vector<std::vector<std::__cxx11::basic_string<char> > > tidysq::find_invalid_letters(const Sq<INTERNAL_IN>&, const SqType&) [with INTERNAL_IN = RCPP_IT]’
72 | return sqapply(sq, ops::OperationFindInvalidLetters<INTERNAL_IN>(sq.alphabet(), dest_type));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
find_invalid_letters.cpp:11:43: required from here
11 | return Rcpp::wrap(find_invalid_letters(import_sq_from_R(x, NA_letter),
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
12 | util::sq_type_for_sq_type_abbr(dest_type)));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../inst/include/tidysq/sqapply.h:13:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘tidysq::LenSq’ {aka ‘long int’} [-Wsign-compare]
13 | for (u_LenSq i = 0; i < vector_in.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c find_motifs.cpp -o find_motifs.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c get_standard_alphabet.cpp -o get_standard_alphabet.o
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq/Rcpp-import.h:3,
from find_motifs.cpp:1:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq.h:5,
from get_standard_alphabet.cpp:3:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c guess_standard_alph.cpp -o guess_standard_alph.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c has.cpp -o has.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c obtain_alphabet.cpp -o obtain_alphabet.o
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq.h:5,
from guess_standard_alph.cpp:1:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq/Rcpp-import.h:3,
from has.cpp:1:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq.h:5,
from obtain_alphabet.cpp:1:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h: In instantiation of ‘VECTOR_OUT tidysq::sqapply(const VECTOR_IN&, ops::OperationVectorToVector<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>&) [with VECTOR_IN = Sq<RCPP_IT>; ELEMENT_IN = Sequence<RCPP_IT>; VECTOR_OUT = std::vector<bool>; ELEMENT_OUT = bool]’:
../inst/include/tidysq/sqapply.h:23:71: required from ‘VECTOR_OUT tidysq::sqapply(const VECTOR_IN&, ops::OperationVectorToVector<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>&&) [with VECTOR_IN = Sq<RCPP_IT>; ELEMENT_IN = Sequence<RCPP_IT>; VECTOR_OUT = std::vector<bool>; ELEMENT_OUT = bool]’
23 | return sqapply<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>(vector_in, operation);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
../inst/include/tidysq/ops/has.h:49:23: required from ‘std::vector<bool> tidysq::has(const Sq<INTERNAL_IN>&, const std::vector<std::__cxx11::basic_string<char> >&) [with INTERNAL_IN = RCPP_IT]’
49 | return sqapply(sq, ops::OperationHas<INTERNAL_IN>(sq.alphabet(), motifs));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
has.cpp:11:34: required from here
11 | return Rcpp::wrap(has<RCPP_IT>(import_sq_from_R(x, NA_letter), motifs));
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../inst/include/tidysq/sqapply.h:13:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘tidysq::LenSq’ {aka ‘long int’} [-Wsign-compare]
13 | for (u_LenSq i = 0; i < vector_in.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c pack.cpp -o pack.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c paste.cpp -o paste.o
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq.h:5,
from pack.cpp:1:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c random_sq.cpp -o random_sq.o
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq.h:5,
from paste.cpp:1:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c read_fasta.cpp -o read_fasta.o
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq/Rcpp-import.h:3,
from random_sq.cpp:4:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq.h:5,
from read_fasta.cpp:3:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c remove_NA.cpp -o remove_NA.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c remove_ambiguous.cpp -o remove_ambiguous.o
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq/Rcpp-import.h:3,
from remove_NA.cpp:3:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq/Rcpp-import.h:3,
from remove_ambiguous.cpp:3:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h: In instantiation of ‘VECTOR_OUT tidysq::sqapply(const VECTOR_IN&, ops::OperationVectorToVector<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>&) [with VECTOR_IN = Sq<RCPP_IT>; ELEMENT_IN = Sequence<RCPP_IT>; VECTOR_OUT = Sq<RCPP_IT>; ELEMENT_OUT = Sequence<RCPP_IT>]’:
../inst/include/tidysq/sqapply.h:23:71: required from ‘VECTOR_OUT tidysq::sqapply(const VECTOR_IN&, ops::OperationVectorToVector<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>&&) [with VECTOR_IN = Sq<RCPP_IT>; ELEMENT_IN = Sequence<RCPP_IT>; VECTOR_OUT = Sq<RCPP_IT>; ELEMENT_OUT = Sequence<RCPP_IT>]’
23 | return sqapply<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>(vector_in, operation);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
../inst/include/tidysq/ops/remove_NA.h:25:23: required from ‘tidysq::Sq<INTERNAL_OUT> tidysq::remove_NA(const Sq<INTERNAL_IN>&, bool) [with INTERNAL_IN = RCPP_IT; INTERNAL_OUT = RCPP_IT]’
25 | return sqapply(sq, ops::OperationRemoveNA<INTERNAL_IN, INTERNAL_OUT>(sq.alphabet(), by_letter));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
remove_NA.cpp:13:42: required from here
13 | return export_to_R(remove_NA<RCPP_IT>(import_sq_from_R(x, NA_letter), by_letter));
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../inst/include/tidysq/sqapply.h:13:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘tidysq::LenSq’ {aka ‘long int’} [-Wsign-compare]
13 | for (u_LenSq i = 0; i < vector_in.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c reverse.cpp -o reverse.o
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h: In instantiation of ‘VECTOR_OUT tidysq::sqapply(const VECTOR_IN&, ops::OperationVectorToVector<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>&) [with VECTOR_IN = Sq<RCPP_IT>; ELEMENT_IN = Sequence<RCPP_IT>; VECTOR_OUT = Sq<RCPP_IT>; ELEMENT_OUT = Sequence<RCPP_IT>]’:
../inst/include/tidysq/sqapply.h:23:71: required from ‘VECTOR_OUT tidysq::sqapply(const VECTOR_IN&, ops::OperationVectorToVector<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>&&) [with VECTOR_IN = Sq<RCPP_IT>; ELEMENT_IN = Sequence<RCPP_IT>; VECTOR_OUT = Sq<RCPP_IT>; ELEMENT_OUT = Sequence<RCPP_IT>]’
23 | return sqapply<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>(vector_in, operation);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
../inst/include/tidysq/ops/remove_ambiguous.h:53:23: required from ‘tidysq::Sq<INTERNAL_OUT> tidysq::remove_ambiguous(const Sq<INTERNAL_IN>&, bool) [with INTERNAL_IN = RCPP_IT; INTERNAL_OUT = RCPP_IT]’
53 | return sqapply(sq, ops::OperationRemoveAmbiguous<INTERNAL_IN, INTERNAL_OUT>(sq.alphabet(), by_letter));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
remove_ambiguous.cpp:13:49: required from here
13 | return export_to_R(remove_ambiguous<RCPP_IT>(import_sq_from_R(x, NA_letter), by_letter));
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../inst/include/tidysq/sqapply.h:13:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘tidysq::LenSq’ {aka ‘long int’} [-Wsign-compare]
13 | for (u_LenSq i = 0; i < vector_in.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c sqapply.cpp -o sqapply.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c substitute_letters.cpp -o substitute_letters.o
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq/Rcpp-import.h:3,
from reverse.cpp:1:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c test-pack.cpp -o test-pack.o
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h: In instantiation of ‘VECTOR_OUT tidysq::sqapply(const VECTOR_IN&, ops::OperationVectorToVector<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>&) [with VECTOR_IN = Sq<RCPP_IT>; ELEMENT_IN = Sequence<RCPP_IT>; VECTOR_OUT = Sq<RCPP_IT>; ELEMENT_OUT = Sequence<RCPP_IT>]’:
../inst/include/tidysq/sqapply.h:23:71: required from ‘VECTOR_OUT tidysq::sqapply(const VECTOR_IN&, ops::OperationVectorToVector<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>&&) [with VECTOR_IN = Sq<RCPP_IT>; ELEMENT_IN = Sequence<RCPP_IT>; VECTOR_OUT = Sq<RCPP_IT>; ELEMENT_OUT = Sequence<RCPP_IT>]’
23 | return sqapply<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>(vector_in, operation);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
../inst/include/tidysq/ops/reverse.h:36:23: required from ‘tidysq::Sq<INTERNAL_OUT> tidysq::reverse(const Sq<INTERNAL_IN>&) [with INTERNAL_IN = RCPP_IT; INTERNAL_OUT = RCPP_IT]’
36 | return sqapply(sq, ops::OperationReverse<INTERNAL_IN, INTERNAL_OUT>(sq.alphabet().alphabet_size()));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
reverse.cpp:10:40: required from here
10 | return export_to_R(reverse<RCPP_IT>(import_sq_from_R(x, NA_letter)));
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../inst/include/tidysq/sqapply.h:13:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘tidysq::LenSq’ {aka ‘long int’} [-Wsign-compare]
13 | for (u_LenSq i = 0; i < vector_in.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq/Rcpp-import.h:3,
from substitute_letters.cpp:3:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c test-runner.cpp -o test-runner.o
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq.h:5,
from test-pack.cpp:3:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h: In instantiation of ‘VECTOR_OUT tidysq::sqapply(const VECTOR_IN&, ops::OperationVectorToVector<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>&) [with VECTOR_IN = Sq<RCPP_IT>; ELEMENT_IN = Sequence<RCPP_IT>; VECTOR_OUT = Sq<RCPP_IT>; ELEMENT_OUT = Sequence<RCPP_IT>]’:
../inst/include/tidysq/sqapply.h:23:71: required from ‘VECTOR_OUT tidysq::sqapply(const VECTOR_IN&, ops::OperationVectorToVector<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>&&) [with VECTOR_IN = Sq<RCPP_IT>; ELEMENT_IN = Sequence<RCPP_IT>; VECTOR_OUT = Sq<RCPP_IT>; ELEMENT_OUT = Sequence<RCPP_IT>]’
23 | return sqapply<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>(vector_in, operation);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
../inst/include/tidysq/ops/substitute_letters.h:98:23: required from ‘tidysq::Sq<INTERNAL_OUT> tidysq::substitute_letters(const Sq<INTERNAL_IN>&, const std::unordered_map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&) [with INTERNAL_IN = RCPP_IT; INTERNAL_OUT = RCPP_IT]’
98 | return sqapply(sq, ops::OperationSubstituteLetters<INTERNAL_IN, INTERNAL_OUT>(sq.alphabet(), encoding));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
substitute_letters.cpp:19:51: required from here
19 | return export_to_R(substitute_letters<RCPP_IT>(import_sq_from_R(x, NA_letter), encoding_map));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../inst/include/tidysq/sqapply.h:13:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘tidysq::LenSq’ {aka ‘long int’} [-Wsign-compare]
13 | for (u_LenSq i = 0; i < vector_in.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
../inst/include/tidysq/ProtoSq.h: In instantiation of ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::RAWS_PT]’:
test-pack.cpp:11:5: required from ‘void test_packing_and_unpacking(const tidysq::ProtoSq<INTERNAL_IN, PROTO_IN>&) [with INTERNAL_UNPACKED = tidysq::RCPP_IT; PROTO = tidysq::RAWS_PT; INTERNAL_PACKED = tidysq::RCPP_IT]’
11 | expect_true(proto_sq == reunpacked);
test-pack.cpp:187:5: required from here
168 | test_packing_and_unpacking<INTERNAL_UNPACKED##_IT, PROTO##_PT, INTERNAL_PACKED##_IT>( \
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
169 | create_proto_sq_from_raws<INTERNAL_UNPACKED##_IT, PROTO##_PT>(alph_##ALPH_SIZE##_sequences, \
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
170 | SIMPLE ? alph_##ALPH_SIZE##_simple : alph_##ALPH_SIZE##_multichar) \
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
171 | ); \
| ~
../inst/include/tidysq/ProtoSq.h:68:34: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
68 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
../inst/include/tidysq/ProtoSq.h: In instantiation of ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::INTS_PT]’:
test-pack.cpp:11:5: required from ‘void test_packing_and_unpacking(const tidysq::ProtoSq<INTERNAL_IN, PROTO_IN>&) [with INTERNAL_UNPACKED = tidysq::RCPP_IT; PROTO = tidysq::INTS_PT; INTERNAL_PACKED = tidysq::RCPP_IT]’
11 | expect_true(proto_sq == reunpacked);
test-pack.cpp:187:5: required from here
168 | test_packing_and_unpacking<INTERNAL_UNPACKED##_IT, PROTO##_PT, INTERNAL_PACKED##_IT>( \
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
169 | create_proto_sq_from_raws<INTERNAL_UNPACKED##_IT, PROTO##_PT>(alph_##ALPH_SIZE##_sequences, \
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
170 | SIMPLE ? alph_##ALPH_SIZE##_simple : alph_##ALPH_SIZE##_multichar) \
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
171 | ); \
| ~
../inst/include/tidysq/ProtoSq.h:68:34: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
68 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
../inst/include/tidysq/ProtoSq.h: In instantiation of ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRINGS_PT]’:
test-pack.cpp:11:5: required from ‘void test_packing_and_unpacking(const tidysq::ProtoSq<INTERNAL_IN, PROTO_IN>&) [with INTERNAL_UNPACKED = tidysq::RCPP_IT; PROTO = tidysq::STRINGS_PT; INTERNAL_PACKED = tidysq::RCPP_IT]’
11 | expect_true(proto_sq == reunpacked);
test-pack.cpp:187:5: required from here
168 | test_packing_and_unpacking<INTERNAL_UNPACKED##_IT, PROTO##_PT, INTERNAL_PACKED##_IT>( \
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
169 | create_proto_sq_from_raws<INTERNAL_UNPACKED##_IT, PROTO##_PT>(alph_##ALPH_SIZE##_sequences, \
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
170 | SIMPLE ? alph_##ALPH_SIZE##_simple : alph_##ALPH_SIZE##_multichar) \
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
171 | ); \
| ~
../inst/include/tidysq/ProtoSq.h:68:34: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
68 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c translate.cpp -o translate.o
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq/Rcpp-import.h:3,
from translate.cpp:1:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c typify.cpp -o typify.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c unpack.cpp -o unpack.o
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h: In instantiation of ‘VECTOR_OUT tidysq::sqapply(const VECTOR_IN&, ops::OperationVectorToVector<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>&) [with VECTOR_IN = Sq<RCPP_IT>; ELEMENT_IN = Sequence<RCPP_IT>; VECTOR_OUT = Sq<RCPP_IT>; ELEMENT_OUT = Sequence<RCPP_IT>]’:
../inst/include/tidysq/sqapply.h:23:71: required from ‘VECTOR_OUT tidysq::sqapply(const VECTOR_IN&, ops::OperationVectorToVector<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>&&) [with VECTOR_IN = Sq<RCPP_IT>; ELEMENT_IN = Sequence<RCPP_IT>; VECTOR_OUT = Sq<RCPP_IT>; ELEMENT_OUT = Sequence<RCPP_IT>]’
23 | return sqapply<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>(vector_in, operation);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
../inst/include/tidysq/ops/translate.h:148:23: required from ‘tidysq::Sq<INTERNAL_OUT> tidysq::translate(const Sq<INTERNAL_IN>&, const unsigned int&) [with INTERNAL_IN = RCPP_IT; INTERNAL_OUT = RCPP_IT]’
148 | return sqapply(sq, ops::OperationTranslate<INTERNAL_IN, INTERNAL_OUT>(table));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
translate.cpp:11:42: required from here
11 | return export_to_R(translate<RCPP_IT>(
| ~~~~~~~~~~~~~~~~~~^
12 | import_sq_from_R(x, NA_letter),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13 | table));
| ~~~~~~
../inst/include/tidysq/sqapply.h:13:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘tidysq::LenSq’ {aka ‘long int’} [-Wsign-compare]
13 | for (u_LenSq i = 0; i < vector_in.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/testthat/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 -c write_fasta.cpp -o write_fasta.o
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq/Rcpp-import.h:3,
from typify.cpp:3:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq.h:5,
from unpack.cpp:3:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
In file included from ../inst/include/tidysq/ops/unpack.h:6,
from ../inst/include/tidysq/Sq.h:5,
from ../inst/include/tidysq.h:5,
from write_fasta.cpp:1:
../inst/include/tidysq/ProtoSq.h: In member function ‘bool tidysq::ProtoSq<INTERNAL, PROTO>::operator==(const tidysq::ProtoSq<INTERNAL, PROTO>&) const [with INTERNAL = tidysq::RCPP_IT; PROTO = tidysq::STRING_PT]’:
../inst/include/tidysq/ProtoSq.h:86:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
86 | for (u_LenSq i = 0; i < content_.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
In file included from ../inst/include/tidysq/ProtoSq.h:5:
../inst/include/tidysq/sqapply.h: In instantiation of ‘VECTOR_OUT tidysq::sqapply(const VECTOR_IN&, ops::OperationVectorToVector<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>&) [with VECTOR_IN = Sq<RCPP_IT>; ELEMENT_IN = Sequence<RCPP_IT>; VECTOR_OUT = Sq<RCPP_IT>; ELEMENT_OUT = Sequence<RCPP_IT>]’:
../inst/include/tidysq/sqapply.h:23:71: required from ‘VECTOR_OUT tidysq::sqapply(const VECTOR_IN&, ops::OperationVectorToVector<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>&&) [with VECTOR_IN = Sq<RCPP_IT>; ELEMENT_IN = Sequence<RCPP_IT>; VECTOR_OUT = Sq<RCPP_IT>; ELEMENT_OUT = Sequence<RCPP_IT>]’
23 | return sqapply<VECTOR_IN, ELEMENT_IN, VECTOR_OUT, ELEMENT_OUT>(vector_in, operation);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
../inst/include/tidysq/ops/typify.h:62:23: required from ‘tidysq::Sq<INTERNAL_OUT> tidysq::typify(const Sq<INTERNAL_IN>&, const SqType&) [with INTERNAL_IN = RCPP_IT; INTERNAL_OUT = RCPP_IT]’
62 | return sqapply(sq, ops::OperationTypify<INTERNAL_IN, INTERNAL_OUT>(sq.alphabet(), dest_type));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
typify.cpp:13:39: required from here
13 | return export_to_R(typify<RCPP_IT>(import_sq_from_R(x, NA_letter),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
14 | util::sq_type_for_sq_type_abbr(dest_type)));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../inst/include/tidysq/sqapply.h:13:31: warning: comparison of integer expressions of different signedness: ‘tidysq::u_LenSq’ {aka ‘long unsigned int’} and ‘tidysq::LenSq’ {aka ‘long int’} [-Wsign-compare]
13 | for (u_LenSq i = 0; i < vector_in.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/testthat/include/testthat/testthat.h:72,
from /data/gannet/ripley/R/test-dev/testthat/include/testthat.h:1,
from test-pack.cpp:1:
test-pack.cpp: In function ‘void ____C_A_T_C_H____T_E_S_T____0()’:
/data/gannet/ripley/R/test-dev/testthat/include/testthat/testthat.h:180:25: note: variable tracking size limit exceeded with ‘-fvar-tracking-assignments’, retrying without
180 | # define context(__X__) CATCH_TEST_CASE(__X__ " | " __FILE__)
| ^~~~~~~~~~~~~~~
test-pack.cpp:95:1: note: in expansion of macro ‘context’
95 | context("test-pack") {
| ^~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o tidysq.so RcppExports.o apply_R_function.o bite.o collapse.o complement.o find_invalid_letters.o find_motifs.o get_standard_alphabet.o guess_standard_alph.o has.o obtain_alphabet.o pack.o paste.o random_sq.o read_fasta.o remove_NA.o remove_ambiguous.o reverse.o sqapply.o substitute_letters.o test-pack.o test-runner.o translate.o typify.o unpack.o write_fasta.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/tidysq/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/tidysq/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/tidysq/src'
installing to /data/gannet/ripley/R/packages/tests-devel/tidysq.Rcheck/00LOCK-tidysq/00new/tidysq/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (tidysq)