############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/Rdisop_1.52.0.tar.gz && rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rdisop.buildbin-libdir Rdisop_1.52.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL Rdisop_1.52.0.zip && rm Rdisop_1.52.0.tar.gz Rdisop_1.52.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 683k 100 683k 0 0 1412k 0 --:--:-- --:--:-- --:--:-- 1415k install for i386 * installing *source* package 'Rdisop' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/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(ims::Element::size_type) const': ./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'unsigned int'} [-Wsign-compare] 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:204:58: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void initializeElements(const Alphabet& alphabet, std::auto_ptr parser) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from disop.cpp:5: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from disop.cpp:26: ./imslib/src/ims/decomp/realmassdecomposer.h:103:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr decomposer; ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from disop.cpp:5: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from disop.cpp:28: ./imslib/src/ims/decomp/decomputils.h: In function 'std::pair ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)': ./imslib/src/ims/decomp/decomputils.h:92:53: warning: typedef 'weight_type' locally defined but not used [-Wunused-local-typedefs] 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] bool parityeven = !parityodd; ^~~~~~~~~~ disop.cpp: In function 'SEXPREC* decomposeIsotopes(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': disop.cpp:228:43: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare] for (peaks_container::size_type i = 0; i < abundances.size(); ++i) { ~~^~~~~~~~~~~~~~~~~~~ disop.cpp:231:43: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare] for (peaks_container::size_type i = 0; i < abundances.size(); ++i) { ~~^~~~~~~~~~~~~~~~~~~ disop.cpp:239:46: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare] for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) { ~~~^~~~~~~~~~~~~~~ disop.cpp:239:68: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare] for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) { ~~~^~~~~~~~~~~~~~~~~~~ disop.cpp:191:6: warning: unused variable 'number_molecules_shown' [-Wunused-variable] int number_molecules_shown = 100; ^~~~~~~~~~~~~~~~~~~~~~ disop.cpp:169:39: warning: typedef 'mass_type' locally defined but not used [-Wunused-local-typedefs] typedef distribution_t::mass_type mass_type; ^~~~~~~~~ disop.cpp:171:47: warning: typedef 'nominal_mass_type' locally defined but not used [-Wunused-local-typedefs] 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] typedef decompositions_t::value_type decomposition_type; ^~~~~~~~~~~~~~~~~~ disop.cpp: In function 'SEXPREC* calculateScore(SEXP, SEXP, SEXP, SEXP)': disop.cpp:390:46: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare] for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) ~~~^~~~~~~~~~~~~~~ disop.cpp:390:68: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare] for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) ~~~^~~~~~~~~~~~~~~~~~~ disop.cpp:407:43: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare] for (peaks_container::size_type i = 0; i < abundances.size(); ++i) { ~~^~~~~~~~~~~~~~~~~~~ disop.cpp:410:43: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare] for (peaks_container::size_type i = 0; i < abundances.size(); ++i) { ~~^~~~~~~~~~~~~~~~~~~ disop.cpp:414:46: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare] for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) ~~~^~~~~~~~~~~~~~~ disop.cpp:414:68: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare] for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) ~~~^~~~~~~~~~~~~~~~~~~ disop.cpp:377:40: warning: typedef 'mass_type' locally defined but not used [-Wunused-local-typedefs] typedef distribution_t::mass_type mass_type; ^~~~~~~~~ disop.cpp: In function 'SEXPREC* rlistScores(std::multimap >, int)': disop.cpp:626:43: warning: typedef 'scorer_type' locally defined but not used [-Wunused-local-typedefs] typedef DistributionProbabilityScorer scorer_type; ^~~~~~~~~~~ disop.cpp: In function 'void initializeCHNOPS(alphabet_t&, int)': disop.cpp:709:32: warning: typedef 'elements_type' locally defined but not used [-Wunused-local-typedefs] 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] typedef alphabet_t::container elements_type; ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/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(ims::Element::size_type) const': ./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i < IsotopeDistribution::SIZE; i++) { ~~^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/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(ims::Element::size_type) const': ./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i < IsotopeDistribution::SIZE; i++) { ~~^~~~~~~~~~~~~~~~~~~~~ In file included from imslib/src/ims/composedelement.cpp:8: ./imslib/src/ims/composedelement.h: At global scope: ./imslib/src/ims/composedelement.h:204:58: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void initializeElements(const Alphabet& alphabet, std::auto_ptr parser) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/composedelement.h:6, from imslib/src/ims/composedelement.cpp:8: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/composedelement.cpp: In constructor 'ims::ComposedElement::ComposedElement(const name_type&, const ims::Alphabet&, unsigned int)': imslib/src/ims/composedelement.cpp:26:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr parser; ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/composedelement.h:6, from imslib/src/ims/composedelement.cpp:8: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/composedelement.cpp:28:17: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] parser = std::auto_ptr(new StandardMoleculeSequenceParser); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/composedelement.h:6, from imslib/src/ims/composedelement.cpp:8: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/composedelement.cpp:30:17: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] parser = std::auto_ptr(new MoleculeSequenceParser); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/composedelement.h:6, from imslib/src/ims/composedelement.cpp:8: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/composedelement.cpp: At global scope: imslib/src/ims/composedelement.cpp:116:73: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void ComposedElement::initializeElements(const Alphabet& alphabet, std::auto_ptr parser) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/composedelement.h:6, from imslib/src/ims/composedelement.cpp:8: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/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(ims::Element::size_type) const': ./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i < IsotopeDistribution::SIZE; i++) { ~~^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/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(ims::Element::size_type) const': ./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i < IsotopeDistribution::SIZE; i++) { ~~^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/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 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/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 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/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 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/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 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/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 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/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 sequence_type&)': imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses] for (; letter_pos < last_pos && ~~~~~~~~~~~~~~~~~~~~~~^~ ( std::isalpha(sequence[letter_pos]) && std::isupper(sequence[letter_pos])) || ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/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 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/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:61:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > countMatches(); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/matchmatrix.h:4, from imslib/src/ims/calib/matchmatrix.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from imslib/src/ims/calib/matchmatrix.cpp:1: ./imslib/src/ims/calib/matchmatrix.h:65:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > countMatchesRestrictive(); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/matchmatrix.h:4, from imslib/src/ims/calib/matchmatrix.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/calib/matchmatrix.cpp:81:6: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > MatchMatrix::countMatches() { ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/matchmatrix.h:4, from imslib/src/ims/calib/matchmatrix.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/calib/matchmatrix.cpp: In member function 'std::auto_ptr > ims::MatchMatrix::countMatches()': imslib/src/ims/calib/matchmatrix.cpp:82:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > m(new std::map); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/matchmatrix.h:4, from imslib/src/ims/calib/matchmatrix.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/calib/matchmatrix.cpp: At global scope: imslib/src/ims/calib/matchmatrix.cpp:102:6: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > MatchMatrix::countMatchesRestrictive() { ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/matchmatrix.h:4, from imslib/src/ims/calib/matchmatrix.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/calib/matchmatrix.cpp: In member function 'std::auto_ptr > ims::MatchMatrix::countMatchesRestrictive()': imslib/src/ims/calib/matchmatrix.cpp:103:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > m(new std::map); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/matchmatrix.h:4, from imslib/src/ims/calib/matchmatrix.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/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:61:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > countMatches(); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/linearpointsetmatcher.h:8, from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ 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:65:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > countMatchesRestrictive(); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/linearpointsetmatcher.h:8, from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: ./imslib/src/ims/calib/linearpointsetmatcher.h:146:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > getMapping() const; ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/linearpointsetmatcher.h:8, from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: ./imslib/src/ims/calib/linearpointsetmatcher.h:169:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > mapping; ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/linearpointsetmatcher.h:8, from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: ./imslib/src/ims/calib/linearpointsetmatcher.h: In member function 'void ims::LinearPointSetMatcher::countMatchesOneToOne(RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, const std::vector&, int, int, float)': ./imslib/src/ims/calib/linearpointsetmatcher.h:281:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > mapping(0); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/linearpointsetmatcher.h:8, from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: ./imslib/src/ims/calib/linearpointsetmatcher.h: In member function 'int ims::LinearPointSetMatcher::match(RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, RandomAccessIterator)': ./imslib/src/ims/calib/linearpointsetmatcher.h:324:26: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] results.mapping = std::auto_ptr >(new std::map); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/linearpointsetmatcher.h:8, from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: ./imslib/src/ims/calib/linearpointsetmatcher.h:326:26: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] results.mapping = std::auto_ptr >(0); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/linearpointsetmatcher.h:8, from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/calib/linearpointsetmatcher.cpp: At global scope: imslib/src/ims/calib/linearpointsetmatcher.cpp:84:6: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > LinearPointSetMatcher::getMapping() const { ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/linearpointsetmatcher.h:8, from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/calib/linearpointsetmatcher.cpp: In member function 'std::auto_ptr > ims::LinearPointSetMatcher::getMapping() const': imslib/src/ims/calib/linearpointsetmatcher.cpp:86:15: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] return std::auto_ptr >(0); // TODO throw sth. instead ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/linearpointsetmatcher.h:8, from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/calib/linearpointsetmatcher.cpp:89:15: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] return std::auto_ptr >(new std::map(*(results.mapping))); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/linearpointsetmatcher.h:8, from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/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:103:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr decomposer; ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/decomp/realmassdecomposer.h:5, from imslib/src/ims/decomp/realmassdecomposer.cpp:8: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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(ims::Element::size_type) const': ./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i < IsotopeDistribution::SIZE; i++) { ~~^~~~~~~~~~~~~~~~~~~~~ In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:9: ./imslib/src/ims/decomp/decomputils.h: In function 'std::pair ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)': ./imslib/src/ims/decomp/decomputils.h:92:53: warning: typedef 'weight_type' locally defined but not used [-Wunused-local-typedefs] 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:21:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] decomposer = std::auto_ptr( ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/decomp/realmassdecomposer.h:5, from imslib/src/ims/decomp/realmassdecomposer.cpp:8: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/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(ims::Element::size_type) const': ./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i < IsotopeDistribution::SIZE; i++) { ~~^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/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(ims::Element::size_type) const': ./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i < IsotopeDistribution::SIZE; i++) { ~~^~~~~~~~~~~~~~~~~~~~~ In file included from ./imslib/src/ims/nitrogenrulefilter.h:4, from imslib/src/ims/nitrogenrulefilter.cpp:5: ./imslib/src/ims/composedelement.h: At global scope: ./imslib/src/ims/composedelement.h:204:58: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void initializeElements(const Alphabet& alphabet, std::auto_ptr parser) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./imslib/src/ims/composedelement.h:6, from ./imslib/src/ims/nitrogenrulefilter.h:4, from imslib/src/ims/nitrogenrulefilter.cpp:5: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ C:/rtools40/mingw32/bin/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:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/Rdisop.buildbin-libdir/00LOCK-Rdisop/00new/Rdisop/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'Rdisop' finding HTML links ... done addMolecules html decomposeMass html getMolecule html initializeCHNOPS html ** 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 install for x64 * installing *source* package 'Rdisop' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/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(ims::Element::size_type) const': ./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 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:204:58: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void initializeElements(const Alphabet& alphabet, std::auto_ptr parser) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from disop.cpp:5: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from disop.cpp:26: ./imslib/src/ims/decomp/realmassdecomposer.h:103:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr decomposer; ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from disop.cpp:5: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from disop.cpp:28: ./imslib/src/ims/decomp/decomputils.h: In function 'std::pair ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)': ./imslib/src/ims/decomp/decomputils.h:92:53: warning: typedef 'weight_type' locally defined but not used [-Wunused-local-typedefs] 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] bool parityeven = !parityodd; ^~~~~~~~~~ disop.cpp: In function 'SEXPREC* decomposeIsotopes(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': disop.cpp:228:43: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] for (peaks_container::size_type i = 0; i < abundances.size(); ++i) { ~~^~~~~~~~~~~~~~~~~~~ disop.cpp:231:43: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] for (peaks_container::size_type i = 0; i < abundances.size(); ++i) { ~~^~~~~~~~~~~~~~~~~~~ disop.cpp:239:46: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) { ~~~^~~~~~~~~~~~~~~ disop.cpp:239:68: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) { ~~~^~~~~~~~~~~~~~~~~~~ disop.cpp:191:6: warning: unused variable 'number_molecules_shown' [-Wunused-variable] int number_molecules_shown = 100; ^~~~~~~~~~~~~~~~~~~~~~ disop.cpp:169:39: warning: typedef 'mass_type' locally defined but not used [-Wunused-local-typedefs] typedef distribution_t::mass_type mass_type; ^~~~~~~~~ disop.cpp:171:47: warning: typedef 'nominal_mass_type' locally defined but not used [-Wunused-local-typedefs] 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] typedef decompositions_t::value_type decomposition_type; ^~~~~~~~~~~~~~~~~~ disop.cpp: In function 'SEXPREC* calculateScore(SEXP, SEXP, SEXP, SEXP)': disop.cpp:390:46: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) ~~~^~~~~~~~~~~~~~~ disop.cpp:390:68: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) ~~~^~~~~~~~~~~~~~~~~~~ disop.cpp:407:43: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] for (peaks_container::size_type i = 0; i < abundances.size(); ++i) { ~~^~~~~~~~~~~~~~~~~~~ disop.cpp:410:43: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] for (peaks_container::size_type i = 0; i < abundances.size(); ++i) { ~~^~~~~~~~~~~~~~~~~~~ disop.cpp:414:46: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) ~~~^~~~~~~~~~~~~~~ disop.cpp:414:68: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) ~~~^~~~~~~~~~~~~~~~~~~ disop.cpp:377:40: warning: typedef 'mass_type' locally defined but not used [-Wunused-local-typedefs] typedef distribution_t::mass_type mass_type; ^~~~~~~~~ disop.cpp: In function 'SEXPREC* rlistScores(std::multimap >, int)': disop.cpp:626:43: warning: typedef 'scorer_type' locally defined but not used [-Wunused-local-typedefs] typedef DistributionProbabilityScorer scorer_type; ^~~~~~~~~~~ disop.cpp: In function 'void initializeCHNOPS(alphabet_t&, int)': disop.cpp:709:32: warning: typedef 'elements_type' locally defined but not used [-Wunused-local-typedefs] 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] typedef alphabet_t::container elements_type; ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/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(ims::Element::size_type) const': ./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i=0; i < IsotopeDistribution::SIZE; i++) { ~~^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/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(ims::Element::size_type) const': ./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i=0; i < IsotopeDistribution::SIZE; i++) { ~~^~~~~~~~~~~~~~~~~~~~~ In file included from imslib/src/ims/composedelement.cpp:8: ./imslib/src/ims/composedelement.h: At global scope: ./imslib/src/ims/composedelement.h:204:58: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void initializeElements(const Alphabet& alphabet, std::auto_ptr parser) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/composedelement.h:6, from imslib/src/ims/composedelement.cpp:8: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/composedelement.cpp: In constructor 'ims::ComposedElement::ComposedElement(const name_type&, const ims::Alphabet&, unsigned int)': imslib/src/ims/composedelement.cpp:26:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr parser; ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/composedelement.h:6, from imslib/src/ims/composedelement.cpp:8: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/composedelement.cpp:28:17: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] parser = std::auto_ptr(new StandardMoleculeSequenceParser); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/composedelement.h:6, from imslib/src/ims/composedelement.cpp:8: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/composedelement.cpp:30:17: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] parser = std::auto_ptr(new MoleculeSequenceParser); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/composedelement.h:6, from imslib/src/ims/composedelement.cpp:8: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/composedelement.cpp: At global scope: imslib/src/ims/composedelement.cpp:116:73: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void ComposedElement::initializeElements(const Alphabet& alphabet, std::auto_ptr parser) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/composedelement.h:6, from imslib/src/ims/composedelement.cpp:8: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/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(ims::Element::size_type) const': ./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i=0; i < IsotopeDistribution::SIZE; i++) { ~~^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/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(ims::Element::size_type) const': ./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i=0; i < IsotopeDistribution::SIZE; i++) { ~~^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/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 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/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 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/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 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/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 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/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 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/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 sequence_type&)': imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses] for (; letter_pos < last_pos && ~~~~~~~~~~~~~~~~~~~~~~^~ ( std::isalpha(sequence[letter_pos]) && std::isupper(sequence[letter_pos])) || ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/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 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:61:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > countMatches(); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/matchmatrix.h:4, from imslib/src/ims/calib/matchmatrix.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from imslib/src/ims/calib/matchmatrix.cpp:1: ./imslib/src/ims/calib/matchmatrix.h:65:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > countMatchesRestrictive(); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/matchmatrix.h:4, from imslib/src/ims/calib/matchmatrix.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/calib/matchmatrix.cpp:81:6: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > MatchMatrix::countMatches() { ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/matchmatrix.h:4, from imslib/src/ims/calib/matchmatrix.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/calib/matchmatrix.cpp: In member function 'std::auto_ptr > ims::MatchMatrix::countMatches()': imslib/src/ims/calib/matchmatrix.cpp:82:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > m(new std::map); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/matchmatrix.h:4, from imslib/src/ims/calib/matchmatrix.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/calib/matchmatrix.cpp: At global scope: imslib/src/ims/calib/matchmatrix.cpp:102:6: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > MatchMatrix::countMatchesRestrictive() { ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/matchmatrix.h:4, from imslib/src/ims/calib/matchmatrix.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/calib/matchmatrix.cpp: In member function 'std::auto_ptr > ims::MatchMatrix::countMatchesRestrictive()': imslib/src/ims/calib/matchmatrix.cpp:103:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > m(new std::map); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/matchmatrix.h:4, from imslib/src/ims/calib/matchmatrix.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:61:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > countMatches(); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/linearpointsetmatcher.h:8, from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ 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:65:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > countMatchesRestrictive(); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/linearpointsetmatcher.h:8, from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: ./imslib/src/ims/calib/linearpointsetmatcher.h:146:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > getMapping() const; ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/linearpointsetmatcher.h:8, from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: ./imslib/src/ims/calib/linearpointsetmatcher.h:169:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > mapping; ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/linearpointsetmatcher.h:8, from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: ./imslib/src/ims/calib/linearpointsetmatcher.h: In member function 'void ims::LinearPointSetMatcher::countMatchesOneToOne(RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, const std::vector&, int, int, float)': ./imslib/src/ims/calib/linearpointsetmatcher.h:281:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > mapping(0); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/linearpointsetmatcher.h:8, from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: ./imslib/src/ims/calib/linearpointsetmatcher.h: In member function 'int ims::LinearPointSetMatcher::match(RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, RandomAccessIterator)': ./imslib/src/ims/calib/linearpointsetmatcher.h:324:26: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] results.mapping = std::auto_ptr >(new std::map); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/linearpointsetmatcher.h:8, from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: ./imslib/src/ims/calib/linearpointsetmatcher.h:326:26: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] results.mapping = std::auto_ptr >(0); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/linearpointsetmatcher.h:8, from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/calib/linearpointsetmatcher.cpp: At global scope: imslib/src/ims/calib/linearpointsetmatcher.cpp:84:6: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > LinearPointSetMatcher::getMapping() const { ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/linearpointsetmatcher.h:8, from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/calib/linearpointsetmatcher.cpp: In member function 'std::auto_ptr > ims::LinearPointSetMatcher::getMapping() const': imslib/src/ims/calib/linearpointsetmatcher.cpp:86:15: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] return std::auto_ptr >(0); // TODO throw sth. instead ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/linearpointsetmatcher.h:8, from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ imslib/src/ims/calib/linearpointsetmatcher.cpp:89:15: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] return std::auto_ptr >(new std::map(*(results.mapping))); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/calib/linearpointsetmatcher.h:8, from imslib/src/ims/calib/linearpointsetmatcher.cpp:11: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/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:103:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr decomposer; ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/decomp/realmassdecomposer.h:5, from imslib/src/ims/decomp/realmassdecomposer.cpp:8: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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(ims::Element::size_type) const': ./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i=0; i < IsotopeDistribution::SIZE; i++) { ~~^~~~~~~~~~~~~~~~~~~~~ In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:9: ./imslib/src/ims/decomp/decomputils.h: In function 'std::pair ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)': ./imslib/src/ims/decomp/decomputils.h:92:53: warning: typedef 'weight_type' locally defined but not used [-Wunused-local-typedefs] 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:21:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] decomposer = std::auto_ptr( ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/decomp/realmassdecomposer.h:5, from imslib/src/ims/decomp/realmassdecomposer.cpp:8: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/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(ims::Element::size_type) const': ./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i=0; i < IsotopeDistribution::SIZE; i++) { ~~^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/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(ims::Element::size_type) const': ./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i=0; i < IsotopeDistribution::SIZE; i++) { ~~^~~~~~~~~~~~~~~~~~~~~ In file included from ./imslib/src/ims/nitrogenrulefilter.h:4, from imslib/src/ims/nitrogenrulefilter.cpp:5: ./imslib/src/ims/composedelement.h: At global scope: ./imslib/src/ims/composedelement.h:204:58: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void initializeElements(const Alphabet& alphabet, std::auto_ptr parser) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./imslib/src/ims/composedelement.h:6, from ./imslib/src/ims/nitrogenrulefilter.h:4, from imslib/src/ims/nitrogenrulefilter.cpp:5: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ C:/rtools40/mingw64/bin/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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/Rdisop.buildbin-libdir/Rdisop/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'Rdisop' as Rdisop_1.52.0.zip * DONE (Rdisop) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'Rdisop' successfully unpacked and MD5 sums checked