installing dependencies ‘enviPat’, ‘Rdisop’ begin installing package ‘enviPat’ begin installing package ‘Rdisop’ * installing *source* package ‘enviPat’ ... ** this is package ‘enviPat’ version ‘2.6’ ** package ‘enviPat’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-9) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpe7af5Z/R.INSTALL1cf32317f32e5/enviPat/src' gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c combination.c -o combination.o gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c element.c -o element.o gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c enviPat_init.c -o enviPat_init.o gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c isotope.c -o isotope.o gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c main.c -o main.o gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c parse.c -o parse.o gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c peak.c -o peak.o gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c profile.c -o profile.o gcc-15 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o enviPat.so combination.o element.o enviPat_init.o isotope.o main.o parse.o peak.o profile.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpe7af5Z/R.INSTALL1cf32317f32e5/enviPat/src' installing to /home/hornik/tmp/CRAN_special_noSuggests/Library/00LOCK-enviPat/00new/enviPat/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (enviPat) * installing *source* package ‘Rdisop’ ... ** this is package ‘Rdisop’ version ‘1.70.0’ ** package ‘Rdisop’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-9) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpK6GqVj/R.INSTALL1cf345f9ee2dc/Rdisop/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -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 unsigned int’} [-Wsign-compare] 166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:92:60: 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:229:50: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 229 | for (peaks_container::size_type i = 0; i < abundances.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~ disop.cpp:232:50: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 232 | for (peaks_container::size_type i = 0; i < abundances.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~ disop.cpp:240:53: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 240 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) { | ~~~^~~~~~~~~~~~~~~ disop.cpp:240:75: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 240 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) { | ~~~^~~~~~~~~~~~~~~~~~~ disop.cpp:192:13: warning: unused variable ‘number_molecules_shown’ [-Wunused-variable] 192 | int number_molecules_shown = 100; | ^~~~~~~~~~~~~~~~~~~~~~ disop.cpp:170:39: warning: typedef ‘mass_type’ locally defined but not used [-Wunused-local-typedefs] 170 | typedef distribution_t::mass_type mass_type; | ^~~~~~~~~ disop.cpp:172:47: warning: typedef ‘nominal_mass_type’ locally defined but not used [-Wunused-local-typedefs] 172 | typedef distribution_t::nominal_mass_type nominal_mass_type; | ^~~~~~~~~~~~~~~~~ disop.cpp:175:42: warning: typedef ‘decomposition_type’ locally defined but not used [-Wunused-local-typedefs] 175 | typedef decompositions_t::value_type decomposition_type; | ^~~~~~~~~~~~~~~~~~ disop.cpp: In function ‘SEXPREC* calculateScore(SEXP, SEXP, SEXP, SEXP)’: disop.cpp:391:53: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 391 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) | ~~~^~~~~~~~~~~~~~~ disop.cpp:391:75: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 391 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) | ~~~^~~~~~~~~~~~~~~~~~~ disop.cpp:408:50: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 408 | for (peaks_container::size_type i = 0; i < abundances.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~ disop.cpp:411:50: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 411 | for (peaks_container::size_type i = 0; i < abundances.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~ disop.cpp:415:53: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 415 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) | ~~~^~~~~~~~~~~~~~~ disop.cpp:415:75: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 415 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) | ~~~^~~~~~~~~~~~~~~~~~~ disop.cpp:378:43: warning: typedef ‘mass_type’ locally defined but not used [-Wunused-local-typedefs] 378 | typedef distribution_t::mass_type mass_type; | ^~~~~~~~~ disop.cpp: In function ‘SEXPREC* rlistScores(std::multimap >, int)’: disop.cpp:627:43: warning: typedef ‘scorer_type’ locally defined but not used [-Wunused-local-typedefs] 627 | typedef DistributionProbabilityScorer scorer_type; | ^~~~~~~~~~~ disop.cpp: In function ‘void initializeCHNOPS(alphabet_t&, int)’: disop.cpp:710:39: warning: typedef ‘elements_type’ locally defined but not used [-Wunused-local-typedefs] 710 | typedef alphabet_t::container elements_type; | ^~~~~~~~~~~~~ disop.cpp: In function ‘void initializeAlphabet(SEXP, alphabet_t&, int)’: disop.cpp:815:33: warning: typedef ‘elements_type’ locally defined but not used [-Wunused-local-typedefs] 815 | typedef alphabet_t::container elements_type; | ^~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -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 unsigned int’} [-Wsign-compare] 166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -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 unsigned int’} [-Wsign-compare] 166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -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 unsigned int’} [-Wsign-compare] 166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -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 unsigned int’} [-Wsign-compare] 166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -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++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o 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 unsigned int’} [-Wsign-compare] 166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./imslib/src/ims/decomp/decomputils.h: In function ‘std::pair 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; | ^~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -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 unsigned int’} [-Wsign-compare] 166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I./imslib/src/ -fpic -g -O2 -Wall -pedantic -mtune=native -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 unsigned int’} [-Wsign-compare] 166 | for (int i=0; i < IsotopeDistribution::SIZE; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o Rdisop.so 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 -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpK6GqVj/R.INSTALL1cf345f9ee2dc/Rdisop/src' installing to /home/hornik/tmp/CRAN_special_noSuggests/Library/00LOCK-Rdisop/00new/Rdisop/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rdisop) checking InterpretMSSpectrum_1.5.2.tar.gz ... Depends: Package: InterpretMSSpectrum Depends: R (>= 2.10.0) Imports: enviPat, plyr Timings: user system elapsed InterpretMSSpectrum 29.223 4.166 35.204 Results: Check status summary: OK Source packages 1 Check results summary: InterpretMSSpectrum ... OK