Install log for 'penPHcure'

* installing *source* package ‘penPHcure’ ...
** package ‘penPHcure’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
using C++11
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/penPHcure/src'
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c cox.base_hazard.cpp -o cox.base_hazard.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c cox.pen.fit.cpp -o cox.pen.fit.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c cox.std.fit.cpp -o cox.std.fit.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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c cure.pen.fit.cpp -o cure.pen.fit.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c cure.simulate.cpp -o cure.simulate.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c cure.std.fit.cpp -o cure.std.fit.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c logit.pen.fit.cpp -o logit.pen.fit.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c logit.std.fit.cpp -o logit.std.fit.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c penPHcure.initialize.cpp -o penPHcure.initialize.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c penalties.cpp -o penalties.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 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -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/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/penPHcure/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/penPHcure/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/penPHcure/src'
installing to /data/gannet/ripley/R/packages/tests-devel/penPHcure.Rcheck/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
* DONE (penPHcure)