downloading reverse dependencies ... downloading archetypal_1.3.1.tar.gz ... ok downloading BDAlgo_0.1.0.tar.gz ... ok downloading matrixcut_0.0.1.tar.gz ... ok downloading RootsExtremaInflections_1.2.5.tar.gz ... ok downloading skedastic_2.0.3.tar.gz ... ok downloading RRmorph_0.0.1.tar.gz ... ok downloading RRphylo_3.0.1.tar.gz ... ok installing dependencies ‘cmna’, ‘ddpcr’, ‘evolqg’, ‘inflection’, ‘lmboot’, ‘mvMORPH’, ‘quadprogXT’, ‘ROI.plugin.qpoases’, ‘Rphylopars’, ‘RRphylo’, ‘smatr’ begin installing package ‘inflection’ begin installing package ‘quadprogXT’ begin installing package ‘ROI.plugin.qpoases’ begin installing package ‘lmboot’ begin installing package ‘cmna’ begin installing package ‘RRphylo’ begin installing package ‘ddpcr’ begin installing package ‘smatr’ begin installing package ‘mvMORPH’ begin installing package ‘evolqg’ begin installing package ‘Rphylopars’ * installing *source* package ‘quadprogXT’ ... ** this is package ‘quadprogXT’ version ‘0.0.6’ ** package ‘quadprogXT’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (quadprogXT) * installing *source* package ‘lmboot’ ... ** this is package ‘lmboot’ version ‘0.0.1’ ** package ‘lmboot’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (lmboot) * installing *source* package ‘inflection’ ... ** this is package ‘inflection’ version ‘1.3.7’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (inflection) * installing *source* package ‘cmna’ ... ** this is package ‘cmna’ version ‘1.0.5’ ** package ‘cmna’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cmna) * installing *source* package ‘smatr’ ... ** this is package ‘smatr’ version ‘3.4-8’ ** package ‘smatr’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (smatr) * installing *source* package ‘ddpcr’ ... ** this is package ‘ddpcr’ version ‘1.15.2’ ** package ‘ddpcr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ddpcr) * installing *source* package ‘RRphylo’ ... ** this is package ‘RRphylo’ version ‘3.0.1’ ** package ‘RRphylo’ 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 ** 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 (RRphylo) * installing *source* package ‘mvMORPH’ ... ** this is package ‘mvMORPH’ version ‘1.2.1’ ** package ‘mvMORPH’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpuhhC5r/R.INSTALL12e388648b62ae/mvMORPH/src' gcc-14 -std=gnu23 -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 chol_rpf_row.c -o chol_rpf_row.o gcc-14 -std=gnu23 -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 chol_rpf_univ.c -o chol_rpf_univ.o gcc-14 -std=gnu23 -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 covar-matrix-simmap.c -o covar-matrix-simmap.o gcc-14 -std=gnu23 -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 givens.c -o givens.o gcc-14 -std=gnu23 -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 kronecker.c -o kronecker.o gcc-14 -std=gnu23 -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 mvMORPH_init.c -o mvMORPH_init.o gcc-14 -std=gnu23 -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 mvmorph-covar-mat.c -o mvmorph-covar-mat.o gcc-14 -std=gnu23 -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 mvmorph-covar-ou-sparse.c -o mvmorph-covar-ou-sparse.o gcc-14 -std=gnu23 -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 mvmorph-covar-ou.c -o mvmorph-covar-ou.o gcc-14 -std=gnu23 -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 mvmorph_ou_mat_rpf.c -o mvmorph_ou_mat_rpf.o gcc-14 -std=gnu23 -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 pic_loglik_mvmorph.c -o pic_loglik_mvmorph.o gcc-14 -std=gnu23 -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 quadprod.c -o quadprod.o gcc-14 -std=gnu23 -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 root2tip.c -o root2tip.o gcc-14 -std=gnu23 -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 spherical.c -o spherical.o gcc-14 -std=gnu23 -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 sqrtMat.c -o sqrtMat.o gcc-14 -std=gnu23 -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 time_serie_expectation.c -o time_serie_expectation.o gcc-14 -std=gnu23 -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 utils.c -o utils.o gcc-14 -std=gnu23 -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 weight-matrix-mvmorph.c -o weight-matrix-mvmorph.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o mvMORPH.so chol_rpf_row.o chol_rpf_univ.o covar-matrix-simmap.o givens.o kronecker.o mvMORPH_init.o mvmorph-covar-mat.o mvmorph-covar-ou-sparse.o mvmorph-covar-ou.o mvmorph_ou_mat_rpf.o pic_loglik_mvmorph.o quadprod.o root2tip.o spherical.o sqrtMat.o time_serie_expectation.o utils.o weight-matrix-mvmorph.o -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpuhhC5r/R.INSTALL12e388648b62ae/mvMORPH/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-mvMORPH/00new/mvMORPH/libs ** R ** data ** 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 (mvMORPH) * installing *source* package ‘evolqg’ ... ** this is package ‘evolqg’ version ‘0.3-4’ ** package ‘evolqg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmptnKoyJ/R.INSTALL12e38cb41a3dc/evolqg/src' g++-14 -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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fast_RS.cpp -o fast_RS.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o evolqg.so RcppExports.o fast_RS.o -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmptnKoyJ/R.INSTALL12e38cb41a3dc/evolqg/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-evolqg/00new/evolqg/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 (evolqg) * installing *source* package ‘ROI.plugin.qpoases’ ... ** this is package ‘ROI.plugin.qpoases’ version ‘1.0-3’ ** package ‘ROI.plugin.qpoases’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmptRV9XX/R.INSTALL12e37c5afff151/ROI.plugin.qpoases/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Iqpoases/include -DLINUX -D__USE_LONG_INTEGERS__ -D__USE_LONG_FINTS__ -DSOLVER_NONE -D__NO_COPYRIGHT__ -D__SUPPRESSANYOUTPUT__ -D__R__ -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c qpoases/src/SQProblem.cpp -o qpoases/src/SQProblem.o In file included from qpoases/include/qpOASES/QProblem.hpp:42, from qpoases/include/qpOASES/SQProblem.hpp:42, from qpoases/src/SQProblem.cpp:37: qpoases/include/qpOASES/QProblemB.hpp:93:36: warning: ‘virtual qpOASES::QProblemB& qpOASES::QProblemB::operator=(const qpOASES::QProblemB&)’ was hidden [-Woverloaded-virtual=] 93 | virtual QProblemB& operator=( const QProblemB& rhs /**< Rhs object. */ | ^~~~~~~~ qpoases/include/qpOASES/QProblem.hpp:93:35: note: by ‘virtual qpOASES::QProblem& qpOASES::QProblem::operator=(const qpOASES::QProblem&)’ 93 | virtual QProblem& operator=( const QProblem& rhs /**< Rhs object. */ | ^~~~~~~~ qpoases/include/qpOASES/QProblem.hpp:93:35: warning: ‘virtual qpOASES::QProblem& qpOASES::QProblem::operator=(const qpOASES::QProblem&)’ was hidden [-Woverloaded-virtual=] qpoases/include/qpOASES/SQProblem.hpp:90:36: note: by ‘virtual qpOASES::SQProblem& qpOASES::SQProblem::operator=(const qpOASES::SQProblem&)’ 90 | virtual SQProblem& operator=( const SQProblem& rhs /**< Rhs object. */ | ^~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Iqpoases/include -DLINUX -D__USE_LONG_INTEGERS__ -D__USE_LONG_FINTS__ -DSOLVER_NONE -D__NO_COPYRIGHT__ -D__SUPPRESSANYOUTPUT__ -D__R__ -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c qpoases/src/QProblem.cpp -o qpoases/src/QProblem.o In file included from qpoases/include/qpOASES/QProblem.hpp:42, from qpoases/src/QProblem.cpp:36: qpoases/include/qpOASES/QProblemB.hpp:93:36: warning: ‘virtual qpOASES::QProblemB& qpOASES::QProblemB::operator=(const qpOASES::QProblemB&)’ was hidden [-Woverloaded-virtual=] 93 | virtual QProblemB& operator=( const QProblemB& rhs /**< Rhs object. */ | ^~~~~~~~ qpoases/include/qpOASES/QProblem.hpp:93:35: note: by ‘virtual qpOASES::QProblem& qpOASES::QProblem::operator=(const qpOASES::QProblem&)’ 93 | virtual QProblem& operator=( const QProblem& rhs /**< Rhs object. */ | ^~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Iqpoases/include -DLINUX -D__USE_LONG_INTEGERS__ -D__USE_LONG_FINTS__ -DSOLVER_NONE -D__NO_COPYRIGHT__ -D__SUPPRESSANYOUTPUT__ -D__R__ -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c qpoases/src/QProblemB.cpp -o qpoases/src/QProblemB.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Iqpoases/include -DLINUX -D__USE_LONG_INTEGERS__ -D__USE_LONG_FINTS__ -DSOLVER_NONE -D__NO_COPYRIGHT__ -D__SUPPRESSANYOUTPUT__ -D__R__ -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c qpoases/src/SQProblemSchur.cpp -o qpoases/src/SQProblemSchur.o In file included from qpoases/include/qpOASES/QProblem.hpp:42, from qpoases/include/qpOASES/SQProblem.hpp:42, from qpoases/include/qpOASES/SQProblemSchur.hpp:42, from qpoases/src/SQProblemSchur.cpp:37: qpoases/include/qpOASES/QProblemB.hpp:93:36: warning: ‘virtual qpOASES::QProblemB& qpOASES::QProblemB::operator=(const qpOASES::QProblemB&)’ was hidden [-Woverloaded-virtual=] 93 | virtual QProblemB& operator=( const QProblemB& rhs /**< Rhs object. */ | ^~~~~~~~ qpoases/include/qpOASES/QProblem.hpp:93:35: note: by ‘virtual qpOASES::QProblem& qpOASES::QProblem::operator=(const qpOASES::QProblem&)’ 93 | virtual QProblem& operator=( const QProblem& rhs /**< Rhs object. */ | ^~~~~~~~ qpoases/include/qpOASES/QProblem.hpp:93:35: warning: ‘virtual qpOASES::QProblem& qpOASES::QProblem::operator=(const qpOASES::QProblem&)’ was hidden [-Woverloaded-virtual=] qpoases/include/qpOASES/SQProblem.hpp:90:36: note: by ‘virtual qpOASES::SQProblem& qpOASES::SQProblem::operator=(const qpOASES::SQProblem&)’ 90 | virtual SQProblem& operator=( const SQProblem& rhs /**< Rhs object. */ | ^~~~~~~~ In file included from qpoases/include/qpOASES/SQProblemSchur.hpp:43: qpoases/include/qpOASES/SparseSolver.hpp:69:39: warning: ‘virtual qpOASES::SparseSolver& qpOASES::SparseSolver::operator=(const qpOASES::SparseSolver&)’ was hidden [-Woverloaded-virtual=] 69 | virtual SparseSolver& operator=( const SparseSolver& rhs /**< Rhs object. */ | ^~~~~~~~ qpoases/include/qpOASES/SparseSolver.hpp:361:7: note: by ‘qpOASES::DummySparseSolver::operator=’ 361 | class DummySparseSolver: public SparseSolver | ^~~~~~~~~~~~~~~~~ qpoases/include/qpOASES/SQProblem.hpp:90:36: warning: ‘virtual qpOASES::SQProblem& qpOASES::SQProblem::operator=(const qpOASES::SQProblem&)’ was hidden [-Woverloaded-virtual=] 90 | virtual SQProblem& operator=( const SQProblem& rhs /**< Rhs object. */ | ^~~~~~~~ qpoases/include/qpOASES/SQProblemSchur.hpp:91:41: note: by ‘virtual qpOASES::SQProblemSchur& qpOASES::SQProblemSchur::operator=(const qpOASES::SQProblemSchur&)’ 91 | virtual SQProblemSchur& operator=( const SQProblemSchur& rhs /**< Rhs object. */ | ^~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Iqpoases/include -DLINUX -D__USE_LONG_INTEGERS__ -D__USE_LONG_FINTS__ -DSOLVER_NONE -D__NO_COPYRIGHT__ -D__SUPPRESSANYOUTPUT__ -D__R__ -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c qpoases/src/Bounds.cpp -o qpoases/src/Bounds.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Iqpoases/include -DLINUX -D__USE_LONG_INTEGERS__ -D__USE_LONG_FINTS__ -DSOLVER_NONE -D__NO_COPYRIGHT__ -D__SUPPRESSANYOUTPUT__ -D__R__ -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c qpoases/src/Constraints.cpp -o qpoases/src/Constraints.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Iqpoases/include -DLINUX -D__USE_LONG_INTEGERS__ -D__USE_LONG_FINTS__ -DSOLVER_NONE -D__NO_COPYRIGHT__ -D__SUPPRESSANYOUTPUT__ -D__R__ -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c qpoases/src/SubjectTo.cpp -o qpoases/src/SubjectTo.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Iqpoases/include -DLINUX -D__USE_LONG_INTEGERS__ -D__USE_LONG_FINTS__ -DSOLVER_NONE -D__NO_COPYRIGHT__ -D__SUPPRESSANYOUTPUT__ -D__R__ -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c qpoases/src/Indexlist.cpp -o qpoases/src/Indexlist.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Iqpoases/include -DLINUX -D__USE_LONG_INTEGERS__ -D__USE_LONG_FINTS__ -DSOLVER_NONE -D__NO_COPYRIGHT__ -D__SUPPRESSANYOUTPUT__ -D__R__ -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c qpoases/src/Flipper.cpp -o qpoases/src/Flipper.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Iqpoases/include -DLINUX -D__USE_LONG_INTEGERS__ -D__USE_LONG_FINTS__ -DSOLVER_NONE -D__NO_COPYRIGHT__ -D__SUPPRESSANYOUTPUT__ -D__R__ -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c qpoases/src/Utils.cpp -o qpoases/src/Utils.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Iqpoases/include -DLINUX -D__USE_LONG_INTEGERS__ -D__USE_LONG_FINTS__ -DSOLVER_NONE -D__NO_COPYRIGHT__ -D__SUPPRESSANYOUTPUT__ -D__R__ -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c qpoases/src/Options.cpp -o qpoases/src/Options.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Iqpoases/include -DLINUX -D__USE_LONG_INTEGERS__ -D__USE_LONG_FINTS__ -DSOLVER_NONE -D__NO_COPYRIGHT__ -D__SUPPRESSANYOUTPUT__ -D__R__ -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c qpoases/src/Matrices.cpp -o qpoases/src/Matrices.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Iqpoases/include -DLINUX -D__USE_LONG_INTEGERS__ -D__USE_LONG_FINTS__ -DSOLVER_NONE -D__NO_COPYRIGHT__ -D__SUPPRESSANYOUTPUT__ -D__R__ -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c qpoases/src/MessageHandling.cpp -o qpoases/src/MessageHandling.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Iqpoases/include -DLINUX -D__USE_LONG_INTEGERS__ -D__USE_LONG_FINTS__ -DSOLVER_NONE -D__NO_COPYRIGHT__ -D__SUPPRESSANYOUTPUT__ -D__R__ -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c qpoases/src/SparseSolver.cpp -o qpoases/src/SparseSolver.o In file included from qpoases/src/SparseSolver.cpp:36: qpoases/include/qpOASES/SparseSolver.hpp:69:39: warning: ‘virtual qpOASES::SparseSolver& qpOASES::SparseSolver::operator=(const qpOASES::SparseSolver&)’ was hidden [-Woverloaded-virtual=] 69 | virtual SparseSolver& operator=( const SparseSolver& rhs /**< Rhs object. */ | ^~~~~~~~ qpoases/include/qpOASES/SparseSolver.hpp:361:7: note: by ‘qpOASES::DummySparseSolver::operator=’ 361 | class DummySparseSolver: public SparseSolver | ^~~~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Iqpoases/include -DLINUX -D__USE_LONG_INTEGERS__ -D__USE_LONG_FINTS__ -DSOLVER_NONE -D__NO_COPYRIGHT__ -D__SUPPRESSANYOUTPUT__ -D__R__ -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c qpoases/src/SolutionAnalysis.cpp -o qpoases/src/SolutionAnalysis.o In file included from qpoases/include/qpOASES/QProblem.hpp:42, from qpoases/include/qpOASES/SQProblem.hpp:42, from qpoases/include/qpOASES/extras/SolutionAnalysis.hpp:40, from qpoases/src/SolutionAnalysis.cpp:37: qpoases/include/qpOASES/QProblemB.hpp:93:36: warning: ‘virtual qpOASES::QProblemB& qpOASES::QProblemB::operator=(const qpOASES::QProblemB&)’ was hidden [-Woverloaded-virtual=] 93 | virtual QProblemB& operator=( const QProblemB& rhs /**< Rhs object. */ | ^~~~~~~~ qpoases/include/qpOASES/QProblem.hpp:93:35: note: by ‘virtual qpOASES::QProblem& qpOASES::QProblem::operator=(const qpOASES::QProblem&)’ 93 | virtual QProblem& operator=( const QProblem& rhs /**< Rhs object. */ | ^~~~~~~~ qpoases/include/qpOASES/QProblem.hpp:93:35: warning: ‘virtual qpOASES::QProblem& qpOASES::QProblem::operator=(const qpOASES::QProblem&)’ was hidden [-Woverloaded-virtual=] qpoases/include/qpOASES/SQProblem.hpp:90:36: note: by ‘virtual qpOASES::SQProblem& qpOASES::SQProblem::operator=(const qpOASES::SQProblem&)’ 90 | virtual SQProblem& operator=( const SQProblem& rhs /**< Rhs object. */ | ^~~~~~~~ In file included from qpoases/include/qpOASES/SQProblemSchur.hpp:43, from qpoases/include/qpOASES/extras/SolutionAnalysis.hpp:41: qpoases/include/qpOASES/SparseSolver.hpp:69:39: warning: ‘virtual qpOASES::SparseSolver& qpOASES::SparseSolver::operator=(const qpOASES::SparseSolver&)’ was hidden [-Woverloaded-virtual=] 69 | virtual SparseSolver& operator=( const SparseSolver& rhs /**< Rhs object. */ | ^~~~~~~~ qpoases/include/qpOASES/SparseSolver.hpp:361:7: note: by ‘qpOASES::DummySparseSolver::operator=’ 361 | class DummySparseSolver: public SparseSolver | ^~~~~~~~~~~~~~~~~ qpoases/include/qpOASES/SQProblem.hpp:90:36: warning: ‘virtual qpOASES::SQProblem& qpOASES::SQProblem::operator=(const qpOASES::SQProblem&)’ was hidden [-Woverloaded-virtual=] 90 | virtual SQProblem& operator=( const SQProblem& rhs /**< Rhs object. */ | ^~~~~~~~ qpoases/include/qpOASES/SQProblemSchur.hpp:91:41: note: by ‘virtual qpOASES::SQProblemSchur& qpOASES::SQProblemSchur::operator=(const qpOASES::SQProblemSchur&)’ 91 | virtual SQProblemSchur& operator=( const SQProblemSchur& rhs /**< Rhs object. */ | ^~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Iqpoases/include -DLINUX -D__USE_LONG_INTEGERS__ -D__USE_LONG_FINTS__ -DSOLVER_NONE -D__NO_COPYRIGHT__ -D__SUPPRESSANYOUTPUT__ -D__R__ -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c qpoases/src/OQPinterface.cpp -o qpoases/src/OQPinterface.o In file included from qpoases/include/qpOASES/QProblem.hpp:42, from qpoases/src/OQPinterface.cpp:40: qpoases/include/qpOASES/QProblemB.hpp:93:36: warning: ‘virtual qpOASES::QProblemB& qpOASES::QProblemB::operator=(const qpOASES::QProblemB&)’ was hidden [-Woverloaded-virtual=] 93 | virtual QProblemB& operator=( const QProblemB& rhs /**< Rhs object. */ | ^~~~~~~~ qpoases/include/qpOASES/QProblem.hpp:93:35: note: by ‘virtual qpOASES::QProblem& qpOASES::QProblem::operator=(const qpOASES::QProblem&)’ 93 | virtual QProblem& operator=( const QProblem& rhs /**< Rhs object. */ | ^~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Iqpoases/include -DLINUX -D__USE_LONG_INTEGERS__ -D__USE_LONG_FINTS__ -DSOLVER_NONE -D__NO_COPYRIGHT__ -D__SUPPRESSANYOUTPUT__ -D__R__ -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c qpoases.cpp -o qpoases.o In file included from qpoases/include/qpOASES.hpp:66, from qpoases.h:4, from qpoases.cpp:2: qpoases/include/qpOASES/QProblemB.hpp:93:36: warning: ‘virtual qpOASES::QProblemB& qpOASES::QProblemB::operator=(const qpOASES::QProblemB&)’ was hidden [-Woverloaded-virtual=] 93 | virtual QProblemB& operator=( const QProblemB& rhs /**< Rhs object. */ | ^~~~~~~~ In file included from qpoases/include/qpOASES.hpp:67: qpoases/include/qpOASES/QProblem.hpp:93:35: note: by ‘virtual qpOASES::QProblem& qpOASES::QProblem::operator=(const qpOASES::QProblem&)’ 93 | virtual QProblem& operator=( const QProblem& rhs /**< Rhs object. */ | ^~~~~~~~ qpoases/include/qpOASES/QProblem.hpp:93:35: warning: ‘virtual qpOASES::QProblem& qpOASES::QProblem::operator=(const qpOASES::QProblem&)’ was hidden [-Woverloaded-virtual=] In file included from qpoases/include/qpOASES.hpp:68: qpoases/include/qpOASES/SQProblem.hpp:90:36: note: by ‘virtual qpOASES::SQProblem& qpOASES::SQProblem::operator=(const qpOASES::SQProblem&)’ 90 | virtual SQProblem& operator=( const SQProblem& rhs /**< Rhs object. */ | ^~~~~~~~ In file included from qpoases/include/qpOASES/SQProblemSchur.hpp:43, from qpoases/include/qpOASES.hpp:69: qpoases/include/qpOASES/SparseSolver.hpp:69:39: warning: ‘virtual qpOASES::SparseSolver& qpOASES::SparseSolver::operator=(const qpOASES::SparseSolver&)’ was hidden [-Woverloaded-virtual=] 69 | virtual SparseSolver& operator=( const SparseSolver& rhs /**< Rhs object. */ | ^~~~~~~~ qpoases/include/qpOASES/SparseSolver.hpp:361:7: note: by ‘qpOASES::DummySparseSolver::operator=’ 361 | class DummySparseSolver: public SparseSolver | ^~~~~~~~~~~~~~~~~ qpoases/include/qpOASES/SQProblem.hpp:90:36: warning: ‘virtual qpOASES::SQProblem& qpOASES::SQProblem::operator=(const qpOASES::SQProblem&)’ was hidden [-Woverloaded-virtual=] 90 | virtual SQProblem& operator=( const SQProblem& rhs /**< Rhs object. */ | ^~~~~~~~ qpoases/include/qpOASES/SQProblemSchur.hpp:91:41: note: by ‘virtual qpOASES::SQProblemSchur& qpOASES::SQProblemSchur::operator=(const qpOASES::SQProblemSchur&)’ 91 | virtual SQProblemSchur& operator=( const SQProblemSchur& rhs /**< Rhs object. */ | ^~~~~~~~ qpoases.cpp: In function ‘SEXPREC* read_oqp_data(std::string)’: qpoases.cpp:389:11: warning: unused variable ‘nQP’ [-Wunused-variable] 389 | int_t nQP, nV, nC, nEC; | ^~~ qpoases.cpp:389:16: warning: unused variable ‘nV’ [-Wunused-variable] 389 | int_t nQP, nV, nC, nEC; | ^~ qpoases.cpp:389:20: warning: unused variable ‘nC’ [-Wunused-variable] 389 | int_t nQP, nV, nC, nEC; | ^~ qpoases.cpp:389:24: warning: unused variable ‘nEC’ [-Wunused-variable] 389 | int_t nQP, nV, nC, nEC; | ^~~ qpoases.cpp:390:17: warning: unused variable ‘path’ [-Wunused-variable] 390 | const char* path = r_path.c_str(); | ^~~~ In file included from /home/hornik/tmp/R/include/R.h:73, from qpoases.h:2: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/exceptions.h: In function ‘void Rcpp::Rf_warning(const char*, Args&& ...) [with Args = {const char*}]’: /home/hornik/tmp/R/include/R_ext/Error.h:85:17: warning: infinite recursion detected [-Winfinite-recursion] 85 | #define warning Rf_warning | ^~~~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/exceptions.h:190:17: note: in expansion of macro ‘warning’ 190 | inline void warning(const char* fmt, Args&&... args ) { | ^~~~~~~ In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:133, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27, from qpoases.h:3: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/exceptions.h:191:19: note: recursive call 191 | Rf_warning("%s", tfm::format(fmt, std::forward(args)... ).c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Iqpoases/include -DLINUX -D__USE_LONG_INTEGERS__ -D__USE_LONG_FINTS__ -DSOLVER_NONE -D__NO_COPYRIGHT__ -D__SUPPRESSANYOUTPUT__ -D__R__ -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o ROI.plugin.qpoases.so qpoases/src/SQProblem.o qpoases/src/QProblem.o qpoases/src/QProblemB.o qpoases/src/SQProblemSchur.o qpoases/src/Bounds.o qpoases/src/Constraints.o qpoases/src/SubjectTo.o qpoases/src/Indexlist.o qpoases/src/Flipper.o qpoases/src/Utils.o qpoases/src/Options.o qpoases/src/Matrices.o qpoases/src/MessageHandling.o qpoases/src/SparseSolver.o qpoases/src/SolutionAnalysis.o qpoases/src/OQPinterface.o qpoases.o RcppExports.o -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmptRV9XX/R.INSTALL12e37c5afff151/ROI.plugin.qpoases/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-ROI.plugin.qpoases/00new/ROI.plugin.qpoases/libs ** R ** 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 (ROI.plugin.qpoases) * installing *source* package ‘Rphylopars’ ... ** this is package ‘Rphylopars’ version ‘0.3.10’ ** package ‘Rphylopars’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpBsii0e/R.INSTALL12e390316d9742/Rphylopars/src' g++-14 -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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c phylopars_rcpp.cpp -o phylopars_rcpp.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o Rphylopars.so RcppExports.o phylopars_rcpp.o -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpBsii0e/R.INSTALL12e390316d9742/Rphylopars/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-Rphylopars/00new/Rphylopars/libs ** R ** 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 (Rphylopars) checking inflection_1.3.7.tar.gz ... checking archetypal_1.3.1.tar.gz ... checking BDAlgo_0.1.0.tar.gz ... checking matrixcut_0.0.1.tar.gz ... checking RootsExtremaInflections_1.2.5.tar.gz ... checking skedastic_2.0.3.tar.gz ... checking RRmorph_0.0.1.tar.gz ... checking RRphylo_3.0.1.tar.gz ... Depends: Package: inflection Imports: parallel, stats, graphics, grDevices Timings: user system elapsed inflection 40.347 4.765 45.728 Results: Check status summary: OK Source packages 1 Reverse depends 7 Check results summary: inflection ... OK rdepends_archetypal ... OK rdepends_BDAlgo ... OK rdepends_matrixcut ... OK rdepends_RootsExtremaInflections ... OK rdepends_RRmorph ... OK rdepends_RRphylo ... OK rdepends_skedastic ... OK Check results changes: Package: matrixcut Check: CRAN incoming feasibility Old result: NOTE