downloading reverse dependencies ‘ASRgenomics’, ‘gpcp’, ‘mappoly’ trying URL 'file:///data/Repositories/CRAN/src/contrib/ASRgenomics_1.1.6.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/gpcp_0.1.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/mappoly_0.4.2.tar.gz' installing dependencies ‘AGHmatrix’, ‘fitPoly’, ‘gatepoints’, ‘polymapR’, ‘updog’ also installing the dependency ‘MDSMap’ begin installing package ‘MDSMap’ begin installing package ‘AGHmatrix’ begin installing package ‘updog’ begin installing package ‘fitPoly’ begin installing package ‘gatepoints’ * installing *source* package ‘gatepoints’ ... ** this is package ‘gatepoints’ version ‘0.1.5’ ** package ‘gatepoints’ 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 (gatepoints) * installing *source* package ‘fitPoly’ ... ** this is package ‘fitPoly’ version ‘4.0.0’ ** package ‘fitPoly’ 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 ** 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 (fitPoly) * installing *source* package ‘MDSMap’ ... ** this is package ‘MDSMap’ version ‘1.3’ ** package ‘MDSMap’ 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 (MDSMap) begin installing package ‘polymapR’ * installing *source* package ‘updog’ ... ** this is package ‘updog’ version ‘2.1.7’ ** package ‘updog’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-16 (Debian 16.1.0-2) 16.1.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp6SiQql/R.INSTALL16df473b21c4cc/updog/src' g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 betabinom.cpp -o betabinom.o g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 em.cpp -o em.o g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 flexdog.cpp -o flexdog.o g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 gradients.cpp -o gradients.o g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 objective.cpp -o objective.o g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 oracle.cpp -o oracle.o g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 util_funs.cpp -o util_funs.o g++-16 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-16/lib -Wl,-O1 -o updog.so RcppExports.o betabinom.o em.o flexdog.o gradients.o objective.o oracle.o util_funs.o -fopenmp -llapack -L/home/hornik/tmp/R-d-gcc-16/lib -lRblas -lgfortran -lm -latomic_asneeded -lquadmath -L/home/hornik/tmp/R-d-gcc-16/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp6SiQql/R.INSTALL16df473b21c4cc/updog/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-updog/00new/updog/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 (updog) * installing *source* package ‘AGHmatrix’ ... ** this is package ‘AGHmatrix’ version ‘3.0.1’ ** using staged installation ** libs using C++ compiler: ‘g++-16 (Debian 16.1.0-2) 16.1.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpCG0hyo/R.INSTALL16df4b21e47478/AGHmatrix/src' g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 amatrix_kerr.cpp -o amatrix_kerr.o g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 amatrix_ploidy2.cpp -o amatrix_ploidy2.o g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 amatrix_slater.cpp -o amatrix_slater.o g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 ascii_to_number.cpp -o ascii_to_number.o g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 check_matrix.cpp -o check_matrix.o g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 datatreat.cpp -o datatreat.o g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 diploid_p0p2_TwoPQ.cpp -o diploid_p0p2_TwoPQ.o g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 dominance_matrix.cpp -o dominance_matrix.o g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 gmatrix_endelman.cpp -o gmatrix_endelman.o gmatrix_endelman.cpp: In function ‘arma::mat Gmatrix_Endelman(const arma::mat&, int)’: gmatrix_endelman.cpp:11:29: warning: unused variable ‘m’ [-Wunused-variable] 11 | const uword n = M.n_rows, m = M.n_cols; | ^ g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 gmatrix_markers_mask.cpp -o gmatrix_markers_mask.o g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 gmatrix_slater.cpp -o gmatrix_slater.o g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 gmatrix_su.cpp -o gmatrix_su.o g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 gmatrix_vanraden.cpp -o gmatrix_vanraden.o g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 gmatrix_vanraden_poly.cpp -o gmatrix_vanraden_poly.o g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 gmatrix_vitezica.cpp -o gmatrix_vitezica.o g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 hmatrix_martini.cpp -o hmatrix_martini.o hmatrix_martini.cpp: In function ‘Rcpp::List H_martini_blocks(const arma::mat&, const arma::mat&, const arma::mat&, double, double)’: hmatrix_martini.cpp:30:15: warning: unused variable ‘n1’ [-Wunused-variable] 30 | const uword n1 = A12.n_rows; | ^~ g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 hmatrix_munoz.cpp -o hmatrix_munoz.o g++-16 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 slater_par.cpp -o slater_par.o g++-16 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-16/lib -Wl,-O1 -o AGHmatrix.so RcppExports.o amatrix_kerr.o amatrix_ploidy2.o amatrix_slater.o ascii_to_number.o check_matrix.o datatreat.o diploid_p0p2_TwoPQ.o dominance_matrix.o gmatrix_endelman.o gmatrix_markers_mask.o gmatrix_slater.o gmatrix_su.o gmatrix_vanraden.o gmatrix_vanraden_poly.o gmatrix_vitezica.o hmatrix_martini.o hmatrix_munoz.o slater_par.o -llapack -L/home/hornik/tmp/R-d-gcc-16/lib -lRblas -lgfortran -lm -latomic_asneeded -lquadmath -fopenmp -L/home/hornik/tmp/R-d-gcc-16/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpCG0hyo/R.INSTALL16df4b21e47478/AGHmatrix/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-AGHmatrix/00new/AGHmatrix/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 (AGHmatrix) * installing *source* package ‘polymapR’ ... ** this is package ‘polymapR’ version ‘1.1.7’ ** package ‘polymapR’ 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 (polymapR) checking AGHmatrix_3.0.1.tar.gz ... checking ASRgenomics_1.1.6.tar.gz ... checking mappoly_0.4.2.tar.gz ... checking gpcp_0.1.0.tar.gz ... Depends: Package: AGHmatrix Depends: R (>= 3.6.0) Imports: Rcpp (>= 1.1.0), matrixStats (>= 1.5.0) LinkingTo: Rcpp, RcppArmadillo Timings: user system elapsed AGHmatrix 227.623 11.416 240.37 Results: Check status summary: OK Source packages 1 Reverse depends 3 Check results summary: AGHmatrix ... OK rdepends_ASRgenomics ... OK rdepends_gpcp ... OK rdepends_mappoly ... OK