downloading reverse dependencies ... downloading do3PCA_1.0.0.tar.gz ... ok installing dependencies ‘mvMORPH’, ‘ratematrix’, ‘Rdimtools’ also installing the dependencies ‘ADMM’, ‘maotai’, ‘mclustcomp’ begin installing package ‘ADMM’ begin installing package ‘maotai’ begin installing package ‘mclustcomp’ begin installing package ‘mvMORPH’ * installing *source* package ‘mclustcomp’ ... ** this is package ‘mclustcomp’ version ‘0.3.5’ ** package ‘mclustcomp’ 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/RtmpRSycPy/R.INSTALL28818c1bf116cb/mclustcomp/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c auxiliary.cpp -o auxiliary.o auxiliary.cpp: In function ‘Rcpp::List getprobs(Rcpp::NumericMatrix, Rcpp::NumericVector, Rcpp::NumericVector, int, double)’: auxiliary.cpp:124:10: warning: unused variable ‘maxthr’ [-Wunused-variable] 124 | double maxthr = max(altthr); | ^~~~~~ auxiliary.cpp:125:7: warning: unused variable ‘warningint’ [-Wunused-variable] 125 | int warningint = 0; // 1<-Px, 2<-Py, 3<-Pxy | ^~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c auxiliary_arma.cpp -o auxiliary_arma.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o mclustcomp.so RcppExports.o auxiliary.o auxiliary_arma.o -fopenmp -llapack -L/home/hornik/tmp/R-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpRSycPy/R.INSTALL28818c1bf116cb/mclustcomp/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-mclustcomp/00new/mclustcomp/libs ** 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 ** 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 (mclustcomp) * 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-15 (Debian 15.2.0-9) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpbkc6mL/R.INSTALL288188cd92845/mvMORPH/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/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-15 -I"/home/hornik/tmp/R-d-gcc-15/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-15 -I"/home/hornik/tmp/R-d-gcc-15/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-15 -I"/home/hornik/tmp/R-d-gcc-15/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-15 -I"/home/hornik/tmp/R-d-gcc-15/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-15 -I"/home/hornik/tmp/R-d-gcc-15/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-15 -I"/home/hornik/tmp/R-d-gcc-15/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-15 -I"/home/hornik/tmp/R-d-gcc-15/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-15 -I"/home/hornik/tmp/R-d-gcc-15/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-15 -I"/home/hornik/tmp/R-d-gcc-15/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-15 -I"/home/hornik/tmp/R-d-gcc-15/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-15 -I"/home/hornik/tmp/R-d-gcc-15/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-15 -I"/home/hornik/tmp/R-d-gcc-15/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-15 -I"/home/hornik/tmp/R-d-gcc-15/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-15 -I"/home/hornik/tmp/R-d-gcc-15/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-15 -I"/home/hornik/tmp/R-d-gcc-15/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-15 -I"/home/hornik/tmp/R-d-gcc-15/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-15 -I"/home/hornik/tmp/R-d-gcc-15/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-15 -shared -L/home/hornik/tmp/R-d-gcc-15/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-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpbkc6mL/R.INSTALL288188cd92845/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) begin installing package ‘ratematrix’ * installing *source* package ‘ADMM’ ... ** this is package ‘ADMM’ version ‘0.3.4’ ** package ‘ADMM’ 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/RtmpDJu6cu/R.INSTALL2881863e8696a1/ADMM/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c src_auxiliary.cpp -o src_auxiliary.o src_auxiliary.cpp: In function ‘arma::cube multipleinversion(arma::mat, double, arma::mat, arma::mat, arma::vec)’: src_auxiliary.cpp:16:13: warning: unused variable ‘n’ [-Wunused-variable] 16 | const int n = A.n_rows; | ^ src_auxiliary.cpp:18:13: warning: unused variable ‘d1’ [-Wunused-variable] 18 | const int d1 = R.n_rows; | ^~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c src_gathered.cpp -o src_gathered.o src_gathered.cpp: In function ‘Rcpp::List admm_bp(const arma::mat&, const arma::colvec&, arma::colvec&, double, double, int, double, double)’: src_gathered.cpp:137:13: warning: unused variable ‘m’ [-Wunused-variable] 137 | const int m = A.n_rows; | ^ src_gathered.cpp: In function ‘arma::mat enet_factor(arma::mat, double)’: src_gathered.cpp:226:13: warning: unused variable ‘m’ [-Wunused-variable] 226 | const int m = A.n_rows; | ^ src_gathered.cpp: In function ‘Rcpp::List admm_enet(const arma::mat&, const arma::colvec&, double, double, double, double, int, double)’: src_gathered.cpp:236:13: warning: unused variable ‘m’ [-Wunused-variable] 236 | const int m = A.n_rows; | ^ src_gathered.cpp: In function ‘arma::mat genlasso_factor(const arma::mat&, double, const arma::mat&)’: src_gathered.cpp:326:13: warning: unused variable ‘m’ [-Wunused-variable] 326 | const int m = A.n_rows; | ^ src_gathered.cpp:327:13: warning: unused variable ‘n’ [-Wunused-variable] 327 | const int n = A.n_cols; | ^ src_gathered.cpp: In function ‘Rcpp::List admm_genlasso(const arma::mat&, const arma::colvec&, const arma::mat&, double, double, double, int, double)’: src_gathered.cpp:335:13: warning: unused variable ‘m’ [-Wunused-variable] 335 | const int m = A.n_rows; | ^ src_gathered.cpp: In function ‘Rcpp::List admm_sdp(arma::mat&, arma::field >&, arma::vec, double, double, double, int, double, bool)’: src_gathered.cpp:929:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 929 | for (int i=0;i= X.n_cols)){ | ~~~~~^~~~~~~~~~~ ver1_nonlinear.cpp:97:7: warning: unused variable ‘P’ [-Wunused-variable] 97 | int P = X.n_cols; | ^ ver1_nonlinear.cpp: In function ‘Rcpp::List dt_rpca(arma::mat&, double, double, int, double)’: ver1_nonlinear.cpp:394:7: warning: unused variable ‘N’ [-Wunused-variable] 394 | int N = X.n_rows; | ^ ver1_nonlinear.cpp:395:7: warning: unused variable ‘P’ [-Wunused-variable] 395 | int P = X.n_cols; | ^ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppDist/include' -I'/home/hornik/tmp/CRAN_recheck/Library/maotai/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ver1_utility.cpp -o ver1_utility.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o Rdimtools.so RcppExports.o Rdimtools_auxiliary.o example_class.o methods_estimation.o methods_handytools.o methods_linear.o methods_nonlinear.o ver1_computation.o ver1_feature.o ver1_linear.o ver1_nonlinear.o ver1_utility.o -fopenmp -llapack -L/home/hornik/tmp/R-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmplUBBH3/R.INSTALL28852ef43b874/Rdimtools/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-Rdimtools/00new/Rdimtools/libs ** 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 ** 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 (Rdimtools) checking ratematrix_1.2.5.tar.gz ... checking do3PCA_1.0.0.tar.gz ... Depends: Package: ratematrix Depends: R (>= 3.5.0) Imports: ape, geiger, coda, corpcor, MASS, phylolm, readr, mvMORPH, Rcpp, ellipse LinkingTo: Rcpp, RcppArmadillo Timings: user system elapsed ratematrix 114.967 10.636 126.994 Results: Check status summary: OK Source packages 1 Reverse depends 1 Check results summary: ratematrix ... OK rdepends_do3PCA ... OK Check results changes: Package: do3PCA Check: package dependencies Old result: ERROR New result: OK