downloading reverse dependencies ‘hwep’, ‘segtest’, ‘ldsep’, ‘mappoly’, ‘polymapR’, ‘Qploidy’ trying URL 'file:///data/Repositories/CRAN/src/contrib/hwep_2.0.3.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/segtest_2.0.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/ldsep_2.1.6.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/mappoly_0.4.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/polymapR_1.1.7.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/Qploidy_1.0.1.tar.gz' installing dependencies ‘AGHmatrix’, ‘fitPoly’, ‘gatepoints’, ‘mappoly’, ‘MDSMap’, ‘polymapR’, ‘polyRAD’, ‘RcppArmadillo’, ‘tensr’, ‘updog’ begin installing package ‘tensr’ begin installing package ‘AGHmatrix’ begin installing package ‘fitPoly’ begin installing package ‘gatepoints’ begin installing package ‘MDSMap’ begin installing package ‘polyRAD’ begin installing package ‘RcppArmadillo’ * 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 ‘tensr’ ... ** this is package ‘tensr’ version ‘1.0.2’ ** package ‘tensr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** 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 (tensr) * installing *source* package ‘AGHmatrix’ ... ** this is package ‘AGHmatrix’ version ‘2.1.4’ ** package ‘AGHmatrix’ 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 (AGHmatrix) * 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 ‘RcppArmadillo’ ... ** this is package ‘RcppArmadillo’ version ‘15.2.4-1’ ** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++-15 -std=gnu++20 accepts -g... yes checking for g++-15 -std=gnu++20 option to enable C++11 features... -std=gnu++11 checking how to run the C++ preprocessor... g++-15 -std=gnu++20 -std=gnu++11 -E checking whether the compiler supports GNU C++... (cached) yes checking whether g++-15 -std=gnu++20 -std=gnu++11 accepts -g... (cached) yes checking for g++-15 -std=gnu++20 -std=gnu++11 option to enable C++11 features... (cached) -std=gnu++11 checking what system we are on... running Linux on x86_64 checking whether we have a suitable tempdir... /home/hornik/tmp/scratch checking whether on Linux... yes checking whether R CMD SHLIB can already compile OpenMP programs... yes checking whether on macOS... no checking for OpenMP... found and suitable configure: creating ./config.status config.status: creating inst/include/RcppArmadillo/config/RcppArmadilloConfigGenerated.h config.status: creating src/Makevars ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-14) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpMw50vM/R.INSTALL339c123565bbc0/RcppArmadillo/src' g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -DARMA_USE_CURRENT -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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppArmadillo.cpp -o RcppArmadillo.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -DARMA_USE_CURRENT -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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -DARMA_USE_CURRENT -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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c fastLm.cpp -o fastLm.o g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.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/RtmpMw50vM/R.INSTALL339c123565bbc0/RcppArmadillo/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-RcppArmadillo/00new/RcppArmadillo/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 (RcppArmadillo) begin installing package ‘mappoly’ begin installing package ‘updog’ * installing *source* package ‘polyRAD’ ... ** this is package ‘polyRAD’ version ‘2.0.0’ ** package ‘polyRAD’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-14) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpDBEkpO/R.INSTALL339c0e7e4f241b/polyRAD/src' g++-15 -std=gnu++20 -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c AdjustAlleleFreq.cpp -o AdjustAlleleFreq.o g++-15 -std=gnu++20 -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c BestGenos.cpp -o BestGenos.o g++-15 -std=gnu++20 -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c FormatStructure.cpp -o FormatStructure.o g++-15 -std=gnu++20 -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c GiniSimpson.cpp -o GiniSimpson.o g++-15 -std=gnu++20 -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c InitHapAssign.cpp -o InitHapAssign.o g++-15 -std=gnu++20 -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PrepVCFexport.cpp -o PrepVCFexport.o g++-15 -std=gnu++20 -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/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++-15 -std=gnu++20 -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SimulateGenotypes.cpp -o SimulateGenotypes.o g++-15 -std=gnu++20 -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ThirdDimProd.cpp -o ThirdDimProd.o g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o polyRAD.so AdjustAlleleFreq.o BestGenos.o FormatStructure.o GiniSimpson.o InitHapAssign.o PrepVCFexport.o RcppExports.o SimulateGenotypes.o ThirdDimProd.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpDBEkpO/R.INSTALL339c0e7e4f241b/polyRAD/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-polyRAD/00new/polyRAD/libs ** R ** data ** 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 (polyRAD) * installing *source* package ‘updog’ ... ** this is package ‘updog’ version ‘2.1.7’ ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-14) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpJYf3tx/R.INSTALL33a1045cfc01e4/updog/src' g++-15 -std=gnu++20 -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/tmp/CRAN_recheck/Library/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++20 -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/tmp/CRAN_recheck/Library/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++-15 -std=gnu++20 -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/tmp/CRAN_recheck/Library/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++-15 -std=gnu++20 -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/tmp/CRAN_recheck/Library/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++-15 -std=gnu++20 -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/tmp/CRAN_recheck/Library/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++-15 -std=gnu++20 -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/tmp/CRAN_recheck/Library/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++-15 -std=gnu++20 -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/tmp/CRAN_recheck/Library/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++-15 -std=gnu++20 -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/tmp/CRAN_recheck/Library/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++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/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-15/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpJYf3tx/R.INSTALL33a1045cfc01e4/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 ‘mappoly’ ... ** this is package ‘mappoly’ version ‘0.4.2’ ** package ‘mappoly’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-14) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-14) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpzvFRDH/R.INSTALL33a1024299303d/mappoly/src' g++-15 -std=gnu++20 -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/RcppParallel/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++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calc_genoprob.cpp -o calc_genoprob.o g++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calc_genoprob_based_on_phased_marker_blocks.cpp -o calc_genoprob_based_on_phased_marker_blocks.o g++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calc_loglike_given_map.cpp -o calc_loglike_given_map.o g++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c combinatorial.cpp -o combinatorial.o g++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c est_hmm_map_based_on_phased_mrk_blocks.cpp -o est_hmm_map_based_on_phased_mrk_blocks.o g++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c est_map_hmm_given_dose.cpp -o est_map_hmm_given_dose.o g++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c est_map_hmm_given_prior.cpp -o est_map_hmm_given_prior.o g++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c genotypic_counts.cpp -o genotypic_counts.o g++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c hmm_elements.cpp -o hmm_elements.o g++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c hmm_single_parent.cpp -o hmm_single_parent.o gcc-15 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mappoly_init.c -o mappoly_init.o g++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pairwise_estimation.cpp -o pairwise_estimation.o g++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pairwise_estimation_rcppparallel.cpp -o pairwise_estimation_rcppparallel.o g++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c read_mappoly_vcf.cpp -o read_mappoly_vcf.o g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o mappoly.so RcppExports.o calc_genoprob.o calc_genoprob_based_on_phased_marker_blocks.o calc_loglike_given_map.o combinatorial.o est_hmm_map_based_on_phased_mrk_blocks.o est_map_hmm_given_dose.o est_map_hmm_given_prior.o genotypic_counts.o hmm_elements.o hmm_single_parent.o mappoly_init.o pairwise_estimation.o pairwise_estimation_rcppparallel.o read_mappoly_vcf.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpzvFRDH/R.INSTALL33a1024299303d/mappoly/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-mappoly/00new/mappoly/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 (mappoly) * 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 updog_2.1.7.tar.gz ... checking hwep_2.0.3.tar.gz ... checking segtest_2.0.0.tar.gz ... checking ldsep_2.1.6.tar.gz ... checking polymapR_1.1.7.tar.gz ... checking mappoly_0.4.2.tar.gz ... checking Qploidy_1.0.1.tar.gz ... Depends: Package: updog Depends: R (>= 3.4.0) Imports: Rcpp (>= 0.12.16), RcppArmadillo, assertthat, ggplot2, reshape2, foreach, future, doFuture, doRNG, methods, iterators, parallelly LinkingTo: Rcpp, RcppArmadillo Timings: user system elapsed updog 128.105 9.16 143.044 Results: Check status summary: OK Source packages 1 Reverse depends 6 Check results summary: updog ... OK rdepends_hwep ... OK rdepends_ldsep ... OK rdepends_mappoly ... OK rdepends_polymapR ... OK rdepends_Qploidy ... OK rdepends_segtest ... OK