Install log for 'Colossus'

* installing *source* package ‘Colossus’ ...
** package ‘Colossus’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (GCC) 14.0.1 20240430 (prerelease)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/Colossus/src'
g++-14 -std=gnu++17 -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/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/testthat/include' -I/usr/local/include    -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 Calc_Repeated.cpp -o Calc_Repeated.o
g++-14 -std=gnu++17 -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/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/testthat/include' -I/usr/local/include    -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 Main_Functions.cpp -o Main_Functions.o
g++-14 -std=gnu++17 -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/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/testthat/include' -I/usr/local/include    -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 Omnibus_Pieces.cpp -o Omnibus_Pieces.o
g++-14 -std=gnu++17 -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/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/testthat/include' -I/usr/local/include    -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 Plot_Extensions.cpp -o Plot_Extensions.o
g++-14 -std=gnu++17 -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/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/testthat/include' -I/usr/local/include    -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 R_Interface.cpp -o R_Interface.o
g++-14 -std=gnu++17 -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/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/testthat/include' -I/usr/local/include    -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++-14 -std=gnu++17 -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/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/testthat/include' -I/usr/local/include    -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 Subterms_Risk.cpp -o Subterms_Risk.o
Calc_Repeated.cpp: In function 'void Calc_LogLik_STRATA_BASIC(const int&, const Rcpp::IntegerMatrix&, const Rcpp::StringMatrix&, const int&, const int&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, std::vector<double>&, std::vector<double>&, std::vector<double>&, bool, std::string, Rcpp::NumericVector&, const Rcpp::IntegerVector&)':
Calc_Repeated.cpp:1571:39: warning: 'Ld1' may be used uninitialized [-Wmaybe-uninitialized]
 1571 |                         Ll[ij] += Ld1 - Rs1;
      |                                   ~~~~^~~~~
Calc_Repeated.cpp:1546:28: note: 'Ld1' was declared here
 1546 |                     double Ld1;
      |                            ^~~
Calc_Repeated.cpp:1572:40: warning: 'Ld2' may be used uninitialized [-Wmaybe-uninitialized]
 1572 |                         Lld[ij] += Ld2 - Rs2;
      |                                    ~~~~^~~~~
Calc_Repeated.cpp:1547:28: note: 'Ld2' was declared here
 1547 |                     double Ld2;
      |                            ^~~
Plot_Extensions.cpp: In function 'Rcpp::List Plot_Omnibus(Rcpp::IntegerVector, Rcpp::StringVector, Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::IntegerVector, int, int, std::string, double, double, Rcpp::NumericMatrix, Rcpp::NumericVector, bool, bool, Rcpp::IntegerVector, int, std::string, int, Rcpp::NumericVector&, Eigen::VectorXd, double, int, bool, bool, bool, bool, bool, bool, bool, double, const Rcpp::IntegerVector&)':
Plot_Extensions.cpp:444:56: warning: 'ijk_risk' may be used uninitialized [-Wmaybe-uninitialized]
  444 |             res_list = List::create(_["x"]=wrap(df0.col(ijk_risk)), _["y"]=wrap(R.col(0)));//returns list of covariate values and risk
      |                                                 ~~~~~~~^~~~~~~~~~
Plot_Extensions.cpp:327:9: note: 'ijk_risk' was declared here
  327 |     int ijk_risk;
      |         ^~~~~~~~
Calc_Repeated.cpp: In function 'void Calc_LogLik_STRATA(const int&, const Rcpp::IntegerMatrix&, const Rcpp::StringMatrix&, const int&, const int&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, std::vector<double>&, std::vector<double>&, std::vector<double>&, bool, std::string, Rcpp::NumericVector&, const Rcpp::IntegerVector&)':
Calc_Repeated.cpp:1412:39: warning: 'Ld1' may be used uninitialized [-Wmaybe-uninitialized]
 1412 |                         Ll[ij] += Ld1 - Rs1;
      |                                   ~~~~^~~~~
Calc_Repeated.cpp:1381:28: note: 'Ld1' was declared here
 1381 |                     double Ld1;
      |                            ^~~
Calc_Repeated.cpp:1413:40: warning: 'Ld2' may be used uninitialized [-Wmaybe-uninitialized]
 1413 |                         Lld[ij] += Ld2 - Rs2;
      |                                    ~~~~^~~~~
Calc_Repeated.cpp:1382:28: note: 'Ld2' was declared here
 1382 |                     double Ld2;
      |                            ^~~
g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o Colossus.so Calc_Repeated.o Main_Functions.o Omnibus_Pieces.o Plot_Extensions.o R_Interface.o RcppExports.o Subterms_Risk.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/Colossus/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/Colossus/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/Colossus/src'
installing to /data/gannet/ripley/R/packages/tests-devel/Colossus.Rcheck/00LOCK-Colossus/00new/Colossus/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 (Colossus)