downloading reverse dependencies ... downloading HiResTEC_0.62.3.tar.gz ... ok installing dependencies ‘CorMID’, ‘InterpretMSSpectrum’, ‘Rdisop’ also installing the dependency ‘enviPat’ begin installing package ‘enviPat’ begin installing package ‘Rdisop’ begin installing package ‘CorMID’ * installing *source* package ‘CorMID’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CorMID) * installing *source* package ‘enviPat’ ... ** package ‘enviPat’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpI1X61X/R.INSTALL1b37a74a273466/enviPat/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -shared -L/home/hornik/tmp/R-d-gcc-14/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-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpI1X61X/R.INSTALL1b37a74a273466/enviPat/src' installing to /home/hornik/tmp/CRAN_recheck/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) begin installing package ‘InterpretMSSpectrum’ * installing *source* package ‘InterpretMSSpectrum’ ... ** package ‘InterpretMSSpectrum’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** 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 * DONE (InterpretMSSpectrum) * installing *source* package ‘Rdisop’ ... ** package ‘Rdisop’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp6HcGeX/R.INSTALL1b37a51139372a/Rdisop/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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:228:50: 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] 228 | for (peaks_container::size_type i = 0; i < abundances.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~ disop.cpp:231:50: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 231 | for (peaks_container::size_type i = 0; i < abundances.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~ disop.cpp:239:53: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 239 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) { | ~~~^~~~~~~~~~~~~~~ disop.cpp:239:75: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 239 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) { | ~~~^~~~~~~~~~~~~~~~~~~ disop.cpp:191:13: warning: unused variable ‘number_molecules_shown’ [-Wunused-variable] 191 | int number_molecules_shown = 100; | ^~~~~~~~~~~~~~~~~~~~~~ disop.cpp:169:39: warning: typedef ‘mass_type’ locally defined but not used [-Wunused-local-typedefs] 169 | typedef distribution_t::mass_type mass_type; | ^~~~~~~~~ disop.cpp:171:47: warning: typedef ‘nominal_mass_type’ locally defined but not used [-Wunused-local-typedefs] 171 | typedef distribution_t::nominal_mass_type nominal_mass_type; | ^~~~~~~~~~~~~~~~~ disop.cpp:174:42: warning: typedef ‘decomposition_type’ locally defined but not used [-Wunused-local-typedefs] 174 | typedef decompositions_t::value_type decomposition_type; | ^~~~~~~~~~~~~~~~~~ disop.cpp: In function ‘SEXPREC* calculateScore(SEXP, SEXP, SEXP, SEXP)’: disop.cpp:390:53: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 390 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) | ~~~^~~~~~~~~~~~~~~ disop.cpp:390:75: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 390 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) | ~~~^~~~~~~~~~~~~~~~~~~ disop.cpp:407:50: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 407 | for (peaks_container::size_type i = 0; i < abundances.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~ disop.cpp:410:50: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 410 | for (peaks_container::size_type i = 0; i < abundances.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~ disop.cpp:414:53: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 414 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) | ~~~^~~~~~~~~~~~~~~ disop.cpp:414:75: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 414 | for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) | ~~~^~~~~~~~~~~~~~~~~~~ disop.cpp:377:43: warning: typedef ‘mass_type’ locally defined but not used [-Wunused-local-typedefs] 377 | typedef distribution_t::mass_type mass_type; | ^~~~~~~~~ disop.cpp: In function ‘SEXPREC* rlistScores(std::multimap >, int)’: disop.cpp:626:43: warning: typedef ‘scorer_type’ locally defined but not used [-Wunused-local-typedefs] 626 | typedef DistributionProbabilityScorer scorer_type; | ^~~~~~~~~~~ disop.cpp: In function ‘void initializeCHNOPS(alphabet_t&, int)’: disop.cpp:709:39: warning: typedef ‘elements_type’ locally defined but not used [-Wunused-local-typedefs] 709 | typedef alphabet_t::container elements_type; | ^~~~~~~~~~~~~ disop.cpp: In function ‘void initializeAlphabet(SEXP, alphabet_t&, int)’: disop.cpp:814:33: warning: typedef ‘elements_type’ locally defined but not used [-Wunused-local-typedefs] 814 | typedef alphabet_t::container elements_type; | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from imslib/src/ims/alphabet.cpp:7: ./imslib/src/ims/utils/compose_f_gx_t.h: At global scope: ./imslib/src/ims/utils/compose_f_gx_t.h:66:16: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 66 | : public std::unary_function struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | : public std::binary_function 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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/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-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp6HcGeX/R.INSTALL1b37a51139372a/Rdisop/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-Rdisop/00new/Rdisop/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** 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 CorMID_0.2.1.tar.gz ... checking HiResTEC_0.62.3.tar.gz ... Depends: Package: CorMID Depends: R (>= 3.50) Imports: Timings: user system elapsed CorMID 37.562 3.73 43.232 Results: Check status summary: OK Source packages 1 Reverse depends 1 Check results summary: CorMID ... OK rdepends_HiResTEC ... OK