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###
### Running command:
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### rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL --build --library=Rdisop.buildbin-libdir Rdisop_1.59.0.tar.gz
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* installing *source* package 'Rdisop' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c disop.cpp -o disop.o
In file included from ./imslib/src/ims/alphabet.h:8,
from disop.cpp:18:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(size_type) const':
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from disop.cpp:22:
./imslib/src/ims/composedelement.h: At global scope:
./imslib/src/ims/composedelement.h:204:72: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
204 | void initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
| ^~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
from ./imslib/src/ims/composedelement.h:6:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from disop.cpp:26:
./imslib/src/ims/decomp/realmassdecomposer.h:103:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
103 | std::auto_ptr<integer_decomposer_type> decomposer;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from disop.cpp:28:
./imslib/src/ims/decomp/decomputils.h: In function 'std::pair<typename DecompositionWeights::alphabet_mass_type, typename DecompositionWeights::alphabet_mass_type> ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)':
./imslib/src/ims/decomp/decomputils.h:92:60: warning: typedef 'weight_type' locally defined but not used [-Wunused-local-typedefs]
92 | typedef typename DecompositionWeights::weight_type weight_type;
| ^~~~~~~~~~~
disop.cpp: In function 'bool isValidMyNitrogenRule(const ims::ComposedElement&, int)':
disop.cpp:106:8: warning: unused variable 'parityeven' [-Wunused-variable]
106 | bool parityeven = !parityodd;
| ^~~~~~~~~~
disop.cpp: In function 'SEXPREC* decomposeIsotopes(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
disop.cpp:228:50: warning: comparison of integer expressions of different signedness: 'std::vector<ims::IsotopeDistribution::Peak>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
228 | for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~~~~
disop.cpp:231:50: warning: comparison of integer expressions of different signedness: 'std::vector<ims::IsotopeDistribution::Peak>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
231 | for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~~~~
disop.cpp:239:53: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
239 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
| ~~~^~~~~~~~~~~~~~~
disop.cpp:239:75: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
239 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
| ~~~^~~~~~~~~~~~~~~~~~~
disop.cpp:325:48: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = multiplies<double>; _Tp = double]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
325 | bind2nd(multiplies<abundance_type>(), scale)); // operation (*scale)
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:1438,
from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\string:48,
from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\locale_classes.h:40,
from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\ios_base.h:41,
from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\ios:42,
from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\ostream:38,
from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\iostream:39,
from disop.cpp:4:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\backward\binders.h:172:5: note: declared here
172 | bind2nd(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
disop.cpp:191:13: warning: unused variable 'number_molecules_shown' [-Wunused-variable]
191 | int number_molecules_shown = 100;
| ^~~~~~~~~~~~~~~~~~~~~~
disop.cpp:169:39: warning: typedef 'mass_type' locally defined but not used [-Wunused-local-typedefs]
169 | typedef distribution_t::mass_type mass_type;
| ^~~~~~~~~
disop.cpp:171:47: warning: typedef 'nominal_mass_type' locally defined but not used [-Wunused-local-typedefs]
171 | typedef distribution_t::nominal_mass_type nominal_mass_type;
| ^~~~~~~~~~~~~~~~~
disop.cpp:174:42: warning: typedef 'decomposition_type' locally defined but not used [-Wunused-local-typedefs]
174 | typedef decompositions_t::value_type decomposition_type;
| ^~~~~~~~~~~~~~~~~~
disop.cpp: In function 'SEXPREC* calculateScore(SEXP, SEXP, SEXP, SEXP)':
disop.cpp:390:53: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
390 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
| ~~~^~~~~~~~~~~~~~~
disop.cpp:390:75: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
390 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
| ~~~^~~~~~~~~~~~~~~~~~~
disop.cpp:407:50: warning: comparison of integer expressions of different signedness: 'std::vector<ims::IsotopeDistribution::Peak>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
407 | for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~~~~
disop.cpp:410:50: warning: comparison of integer expressions of different signedness: 'std::vector<ims::IsotopeDistribution::Peak>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
410 | for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~~~~
disop.cpp:414:53: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
414 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
| ~~~^~~~~~~~~~~~~~~
disop.cpp:414:75: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
414 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
| ~~~^~~~~~~~~~~~~~~~~~~
disop.cpp:377:43: warning: typedef 'mass_type' locally defined but not used [-Wunused-local-typedefs]
377 | typedef distribution_t::mass_type mass_type;
| ^~~~~~~~~
disop.cpp: In function 'SEXPREC* rlistScores(std::multimap<score_type, ims::ComposedElement, std::greater<score_type> >, int)':
disop.cpp:626:43: warning: typedef 'scorer_type' locally defined but not used [-Wunused-local-typedefs]
626 | typedef DistributionProbabilityScorer scorer_type;
| ^~~~~~~~~~~
disop.cpp: In function 'void initializeCHNOPS(alphabet_t&, int)':
disop.cpp:709:39: warning: typedef 'elements_type' locally defined but not used [-Wunused-local-typedefs]
709 | typedef alphabet_t::container elements_type;
| ^~~~~~~~~~~~~
disop.cpp: In function 'void initializeAlphabet(SEXP, alphabet_t&, int)':
disop.cpp:814:33: warning: typedef 'elements_type' locally defined but not used [-Wunused-local-typedefs]
814 | typedef alphabet_t::container elements_type;
| ^~~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
In file included from imslib/src/ims/element.cpp:6:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(size_type) const':
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
In file included from ./imslib/src/ims/composedelement.h:7,
from imslib/src/ims/composedelement.cpp:8:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(size_type) const':
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
./imslib/src/ims/composedelement.h: At global scope:
./imslib/src/ims/composedelement.h:204:72: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
204 | void initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
| ^~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
from ./imslib/src/ims/composedelement.h:6:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
imslib/src/ims/composedelement.cpp: In constructor 'ims::ComposedElement::ComposedElement(const ims::Element::name_type&, const ims::Alphabet&, unsigned int)':
imslib/src/ims/composedelement.cpp:26:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
26 | std::auto_ptr<sequence_parser_type> parser;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
imslib/src/ims/composedelement.cpp:28:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
28 | parser = std::auto_ptr<sequence_parser_type>(new StandardMoleculeSequenceParser);
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
imslib/src/ims/composedelement.cpp:30:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
30 | parser = std::auto_ptr<sequence_parser_type>(new MoleculeSequenceParser);
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
imslib/src/ims/composedelement.cpp: At global scope:
imslib/src/ims/composedelement.cpp:116:73: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
116 | void ComposedElement::initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
In file included from ./imslib/src/ims/alphabet.h:8,
from imslib/src/ims/alphabet.cpp:6:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(size_type) const':
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from imslib/src/ims/alphabet.cpp:7:
./imslib/src/ims/utils/compose_f_gx_t.h: At global scope:
./imslib/src/ims/utils/compose_f_gx_t.h:66:16: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
66 | : public std::unary_function<typename OP2::argument_type,
| ^~~~~~~~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\functional:49,
from imslib/src/ims/alphabet.cpp:4:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from imslib/src/ims/alphabet.cpp:8:
./imslib/src/ims/utils/compose_f_gx_hy_t.h:57:16: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
57 | : public std::binary_function<typename OP2::argument_type,
| ^~~~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
imslib/src/ims/alphabet.cpp: In member function 'bool ims::Alphabet::hasName(const name_type&) const':
imslib/src/ims/alphabet.cpp:33:42: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to<__cxx11::basic_string<char> >; _Tp = __cxx11::basic_string<char>]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
33 | compose_f_gx(std::bind2nd(std::equal_to<name_type>(), name),
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:1438:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\backward\binders.h:172:5: note: declared here
172 | bind2nd(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
imslib/src/ims/alphabet.cpp:34:33: warning: 'std::const_mem_fun_ref_t<_Ret, _Tp> std::mem_fun_ref(_Ret (_Tp::*)() const) [with _Ret = const __cxx11::basic_string<char>&; _Tp = ims::Element]' is deprecated: use 'std::mem_fn' instead [-Wdeprecated-declarations]
34 | std::mem_fun_ref(&element_type::getName))) < elements.end();
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:1389:5: note: declared here
1389 | mem_fun_ref(_Ret (_Tp::*__f)() const)
| ^~~~~~~~~~~
imslib/src/ims/alphabet.cpp: In member function 'virtual void ims::Alphabet::sortByNames()':
imslib/src/ims/alphabet.cpp:74:57: warning: 'std::const_mem_fun_ref_t<_Ret, _Tp> std::mem_fun_ref(_Ret (_Tp::*)() const) [with _Ret = const __cxx11::basic_string<char>&; _Tp = ims::Element]' is deprecated: use 'std::mem_fn' instead [-Wdeprecated-declarations]
74 | std::mem_fun_ref(&element_type::getName),
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:1389:5: note: declared here
1389 | mem_fun_ref(_Ret (_Tp::*__f)() const)
| ^~~~~~~~~~~
imslib/src/ims/alphabet.cpp:75:57: warning: 'std::const_mem_fun_ref_t<_Ret, _Tp> std::mem_fun_ref(_Ret (_Tp::*)() const) [with _Ret = const __cxx11::basic_string<char>&; _Tp = ims::Element]' is deprecated: use 'std::mem_fn' instead [-Wdeprecated-declarations]
75 | std::mem_fun_ref(&element_type::getName)));
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:1389:5: note: declared here
1389 | mem_fun_ref(_Ret (_Tp::*__f)() const)
| ^~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
In file included from ./imslib/src/ims/alphabet.h:8,
from ./imslib/src/ims/distributedalphabet.h:7,
from imslib/src/ims/distributedalphabet.cpp:7:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(size_type) const':
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp: In member function 'virtual void ims::KeggLigandCompoundsParser::parse(const ims::AbstractMoleculeSequenceParser::sequence_type&)':
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:39: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
53 | for (; letter_pos < last_pos &&
| ~~~~~~~~~~~~~~~~~~~~~~^~
54 | ( std::isalpha(sequence[letter_pos]) && std::isupper(sequence[letter_pos])) ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
In file included from imslib/src/ims/calib/matchmatrix.cpp:1:
./imslib/src/ims/calib/matchmatrix.h:61:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
61 | std::auto_ptr<std::map<int,int> > countMatches();
| ^~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
from ./imslib/src/ims/calib/matchmatrix.h:4:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./imslib/src/ims/calib/matchmatrix.h:65:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
65 | std::auto_ptr<std::map<int,int> > countMatchesRestrictive();
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
imslib/src/ims/calib/matchmatrix.cpp:81:6: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
81 | std::auto_ptr<std::map<int,int> > MatchMatrix::countMatches() {
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
imslib/src/ims/calib/matchmatrix.cpp: In member function 'std::auto_ptr<std::map<int, int> > ims::MatchMatrix::countMatches()':
imslib/src/ims/calib/matchmatrix.cpp:82:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
82 | std::auto_ptr<std::map<int,int> > m(new std::map<int,int>);
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
imslib/src/ims/calib/matchmatrix.cpp: At global scope:
imslib/src/ims/calib/matchmatrix.cpp:102:6: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
102 | std::auto_ptr<std::map<int,int> > MatchMatrix::countMatchesRestrictive() {
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
imslib/src/ims/calib/matchmatrix.cpp: In member function 'std::auto_ptr<std::map<int, int> > ims::MatchMatrix::countMatchesRestrictive()':
imslib/src/ims/calib/matchmatrix.cpp:103:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
103 | std::auto_ptr<std::map<int,int> > m(new std::map<int,int>);
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
In file included from ./imslib/src/ims/calib/linearpointsetmatcher.h:13,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./imslib/src/ims/calib/matchmatrix.h:61:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
61 | std::auto_ptr<std::map<int,int> > countMatches();
| ^~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./imslib/src/ims/calib/matchmatrix.h:65:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
65 | std::auto_ptr<std::map<int,int> > countMatchesRestrictive();
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./imslib/src/ims/calib/linearpointsetmatcher.h:146:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
146 | std::auto_ptr<std::map<int,int> > getMapping() const;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./imslib/src/ims/calib/linearpointsetmatcher.h:169:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
169 | std::auto_ptr<std::map<int,int> > mapping;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./imslib/src/ims/calib/linearpointsetmatcher.h: In member function 'void ims::LinearPointSetMatcher::countMatchesOneToOne(RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, const std::vector<ims::RepresentativeScale>&, int, int, float)':
./imslib/src/ims/calib/linearpointsetmatcher.h:281:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
281 | std::auto_ptr<std::map<int,int> > mapping(0);
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./imslib/src/ims/calib/linearpointsetmatcher.h: In member function 'int ims::LinearPointSetMatcher::match(RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, RandomAccessIterator)':
./imslib/src/ims/calib/linearpointsetmatcher.h:324:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
324 | results.mapping = std::auto_ptr<std::map<int,int> >(new std::map<int,int>);
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./imslib/src/ims/calib/linearpointsetmatcher.h:326:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
326 | results.mapping = std::auto_ptr<std::map<int,int> >(0);
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
imslib/src/ims/calib/linearpointsetmatcher.cpp: At global scope:
imslib/src/ims/calib/linearpointsetmatcher.cpp:84:6: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
84 | std::auto_ptr<std::map<int,int> > LinearPointSetMatcher::getMapping() const {
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
imslib/src/ims/calib/linearpointsetmatcher.cpp: In member function 'std::auto_ptr<std::map<int, int> > ims::LinearPointSetMatcher::getMapping() const':
imslib/src/ims/calib/linearpointsetmatcher.cpp:86:29: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
86 | return std::auto_ptr<std::map<int,int> >(0); // TODO throw sth. instead
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
imslib/src/ims/calib/linearpointsetmatcher.cpp:89:29: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
89 | return std::auto_ptr<std::map<int,int> >(new std::map<int,int>(*(results.mapping)));
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:8:
./imslib/src/ims/decomp/realmassdecomposer.h:103:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
103 | std::auto_ptr<integer_decomposer_type> decomposer;
| ^~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
from ./imslib/src/ims/decomp/realmassdecomposer.h:5:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./imslib/src/ims/alphabet.h:8,
from ./imslib/src/ims/decomp/decomputils.h:12,
from imslib/src/ims/decomp/realmassdecomposer.cpp:9:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(size_type) const':
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
./imslib/src/ims/decomp/decomputils.h: In function 'std::pair<typename DecompositionWeights::alphabet_mass_type, typename DecompositionWeights::alphabet_mass_type> ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)':
./imslib/src/ims/decomp/decomputils.h:92:60: warning: typedef 'weight_type' locally defined but not used [-Wunused-local-typedefs]
92 | typedef typename DecompositionWeights::weight_type weight_type;
| ^~~~~~~~~~~
imslib/src/ims/decomp/realmassdecomposer.cpp: In constructor 'ims::RealMassDecomposer::RealMassDecomposer(const ims::Weights&)':
imslib/src/ims/decomp/realmassdecomposer.cpp:21:27: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
21 | decomposer = std::auto_ptr<integer_decomposer_type>(
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
In file included from ./imslib/src/ims/alphabet.h:8,
from ./imslib/src/ims/characteralphabet.h:6,
from imslib/src/ims/characteralphabet.cpp:3:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(size_type) const':
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
In file included from ./imslib/src/ims/composedelement.h:7,
from ./imslib/src/ims/nitrogenrulefilter.h:4,
from imslib/src/ims/nitrogenrulefilter.cpp:5:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(size_type) const':
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
./imslib/src/ims/composedelement.h: At global scope:
./imslib/src/ims/composedelement.h:204:72: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
204 | void initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
| ^~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
from ./imslib/src/ims/composedelement.h:6:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++11 -shared -s -static-libgcc -o Rdisop.dll tmp.def disop.o imslib/src/ims/element.o imslib/src/ims/composedelement.o imslib/src/ims/isotopedistribution.o imslib/src/ims/alphabet.o imslib/src/ims/weights.o imslib/src/ims/distributedalphabet.o imslib/src/ims/transformation.o imslib/src/ims/isotopespecies.o imslib/src/ims/base/parser/alphabettextparser.o imslib/src/ims/base/parser/distributedalphabettextparser.o imslib/src/ims/base/parser/massestextparser.o imslib/src/ims/base/parser/moleculesequenceparser.o imslib/src/ims/base/parser/standardmoleculesequenceparser.o imslib/src/ims/base/parser/keggligandcompoundsparser.o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o imslib/src/ims/calib/linepairstabber.o imslib/src/ims/calib/matchmatrix.o imslib/src/ims/calib/linearpointsetmatcher.o imslib/src/ims/decomp/realmassdecomposer.o imslib/src/ims/utils/distribution.o imslib/src/ims/distributionprobabilityscorer.o imslib/src/ims/characteralphabet.o imslib/src/ims/nitrogenrulefilter.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Rdisop.buildbin-libdir/00LOCK-Rdisop/00new/Rdisop/libs/x64
** R
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'Rdisop' as Rdisop_1.59.0.zip
* DONE (Rdisop)