* installing to library ‘/home/hornik/tmp/R.check/r-patched-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 '/tmp/Rtmp4MWNeE/R.INSTALL940a23f4aac46/penPHcure/src'
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-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-patched-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-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmp4MWNeE/R.INSTALL940a23f4aac46/penPHcure/src'
make[1]: Entering directory '/tmp/Rtmp4MWNeE/R.INSTALL940a23f4aac46/penPHcure/src'
make[1]: Leaving directory '/tmp/Rtmp4MWNeE/R.INSTALL940a23f4aac46/penPHcure/src'
installing to /home/hornik/tmp/R.check/r-patched-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
converting help for package ‘penPHcure’
finding HTML links ... done
PHcure.object html
cpRossi html
penPHcure-package html
penPHcure html
penPHcure.object html
penPHcure.simulate html
predict.PHcure html
predict.penPHcure html
summary.PHcure html
summary.penPHcure html
** 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 (penPHcure)