* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’ * installing *source* package ‘penPHcure’ ... ** package ‘penPHcure’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp6GXWdr/R.INSTALL19e33b75062f82/penPHcure/src' g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c cox.base_hazard.cpp -o cox.base_hazard.o cox.base_hazard.cpp: In function ‘arma::vec cox_base_hazard_cpp(const arma::vec&, const arma::uword&, const arma::uword&, const arma::vec&, const arma::vec&, const arma::uvec&, const arma::uvec&, const arma::uvec&, const arma::mat&, const arma::vec&, const arma::uword&)’: cox.base_hazard.cpp:66:9: warning: ‘dtime’ may be used uninitialized [-Wmaybe-uninitialized] 66 | if (start[p1] < dtime) break; | ^~ cox.base_hazard.cpp:39:10: note: ‘dtime’ was declared here 39 | double dtime,risk,denom2; | ^~~~~ g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c cox.pen.fit.cpp -o cox.pen.fit.o g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c cox.std.fit.cpp -o cox.std.fit.o cox.std.fit.cpp: In function ‘double logL_cox_cpp(const arma::vec&, const arma::uword&, const arma::uword&, const arma::vec&, const arma::vec&, const arma::uvec&, const arma::uvec&, const arma::uvec&, const arma::mat&, const arma::vec&, const arma::uword&)’: cox.std.fit.cpp:64:9: warning: ‘dtime’ may be used uninitialized [-Wmaybe-uninitialized] 64 | if (start[p1] < dtime) break; | ^~ cox.std.fit.cpp:43:10: note: ‘dtime’ was declared here 43 | double dtime,risk,denom2; | ^~~~~ cox.std.fit.cpp: In function ‘void logLgradHess_cox_cpp(double&, arma::vec&, arma::mat&, const arma::vec&, const arma::uword&, const arma::uword&, const arma::vec&, const arma::vec&, const arma::uvec&, const arma::uvec&, const arma::uvec&, const arma::mat&, const arma::vec&, const arma::uword&)’: cox.std.fit.cpp:154:9: warning: ‘dtime’ may be used uninitialized [-Wmaybe-uninitialized] 154 | if (start[p1] < dtime) break; | ^~ cox.std.fit.cpp:126:10: note: ‘dtime’ was declared here 126 | double dtime,risk,denom2; | ^~~~~ g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c cure.pen.fit.cpp -o cure.pen.fit.o g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c cure.simulate.cpp -o cure.simulate.o g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c cure.std.fit.cpp -o cure.std.fit.o g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c logit.pen.fit.cpp -o logit.pen.fit.o g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c logit.std.fit.cpp -o logit.std.fit.o g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c penPHcure.initialize.cpp -o penPHcure.initialize.o g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c penalties.cpp -o penalties.o g++-13 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o penPHcure.so RcppExports.o cox.base_hazard.o cox.pen.fit.o cox.std.fit.o cure.pen.fit.o cure.simulate.o cure.std.fit.o logit.pen.fit.o logit.std.fit.o penPHcure.initialize.o penalties.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp6GXWdr/R.INSTALL19e33b75062f82/penPHcure/src' make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp6GXWdr/R.INSTALL19e33b75062f82/penPHcure/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp6GXWdr/R.INSTALL19e33b75062f82/penPHcure/src' installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-penPHcure/00new/penPHcure/libs ** R ** data *** moving datasets to lazyload DB ** 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 * creating tarball packaged installation of ‘penPHcure’ as ‘penPHcure_1.0.2_R_x86_64-pc-linux-gnu.tar.gz’ * DONE (penPHcure)