* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘Phase123’ ...
** package ‘Phase123’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-25) 13.2.0’
make[1]: Entering directory '/tmp/Rtmp1kCnP8/R.INSTALL24d0c9944ccc/Phase123/src'
g++-13 -std=gnu++17 -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 PHASE123CODE.cpp -o PHASE123CODE.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:26,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
                 from PHASE123CODE.cpp:5:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:326:86: note: ‘#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed’
  326 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |                                                                                      ^
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:331:75: note: ‘#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead’
  331 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |                                                                           ^
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:334:61: note: ‘#pragma message: INFO: see the documentation for details’
  334 |   #pragma message ("INFO: see the documentation for details")
      |                                                             ^
PHASE123CODE.cpp: In function ‘double Like(arma::vec, arma::vec, arma::vec, arma::vec, double, int)’:
PHASE123CODE.cpp:130:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  130 |   for(i=0;i<YE.n_rows;i++){
      |           ~^~~~~~~~~~
PHASE123CODE.cpp:106:7: warning: unused variable ‘m’ [-Wunused-variable]
  106 |   int m=0;
      |       ^
PHASE123CODE.cpp: In function ‘double Like2(arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, int)’:
PHASE123CODE.cpp:212:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  212 |   for(m=0;m<Y.n_rows;m++){
      |           ~^~~~~~~~~
PHASE123CODE.cpp:223:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  223 |     for(m=0; m<Y.n_rows;m++){
      |              ~^~~~~~~~~
PHASE123CODE.cpp: In function ‘double GetMin(arma::vec)’:
PHASE123CODE.cpp:313:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  313 |   for(j=1;j<DESIRE.n_rows;j++){
      |           ~^~~~~~~~~~~~~~
PHASE123CODE.cpp: In function ‘int GetDose1(arma::vec)’:
PHASE123CODE.cpp:403:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  403 |   for(j=0;j<DESIRE.n_rows;j++){
      |           ~^~~~~~~~~~~~~~
PHASE123CODE.cpp:464:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  464 |         if(which1==(cumprob.n_rows-1)){
      |            ~~~~~~^~~~~~~~~~~~~~~~~~~~
PHASE123CODE.cpp: In function ‘Rcpp::List RunAdaptiveEffToxTrial(int, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, int, int, int, int, int, arma::vec, arma::vec)’:
PHASE123CODE.cpp:867:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  867 |           for(j=0;j<Dose.n_rows;j++){
      |                   ~^~~~~~~~~~~~
PHASE123CODE.cpp:912:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  912 |       for(j=0;j<Dose.n_rows;j++){
      |               ~^~~~~~~~~~~~
PHASE123CODE.cpp:930:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  930 |       for(j=0;j<Dose.n_rows;j++){
      |               ~^~~~~~~~~~~~
PHASE123CODE.cpp:949:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  949 |       for(j=0;j<Dose.n_rows;j++){
      |               ~^~~~~~~~~~~~
PHASE123CODE.cpp:980:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  980 |           for(j=1;j<Dose.n_rows;j++){
      |                   ~^~~~~~~~~~~~
PHASE123CODE.cpp:1001:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1001 |           for(j=0;j<Dose.n_rows;j++){
      |                   ~^~~~~~~~~~~~
PHASE123CODE.cpp:1008:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1008 |           for(j=1;j<Dose.n_rows;j++){
      |                   ~^~~~~~~~~~~~
PHASE123CODE.cpp:1022:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1022 |             for(j=1;j<Dose.n_rows;j++){
      |                     ~^~~~~~~~~~~~
PHASE123CODE.cpp:1233:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1233 |           for(j=0;j<Dose.n_rows;j++){
      |                   ~^~~~~~~~~~~~
PHASE123CODE.cpp:1278:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1278 |       for(j=0;j<Dose.n_rows;j++){
      |               ~^~~~~~~~~~~~
PHASE123CODE.cpp:1297:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1297 |       for(j=0;j<Dose.n_rows;j++){
      |               ~^~~~~~~~~~~~
PHASE123CODE.cpp:1318:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1318 |       for(j=0;j<Dose.n_rows;j++){
      |               ~^~~~~~~~~~~~
PHASE123CODE.cpp:1340:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1340 |         for(j=1;j<Dose.n_rows;j++){
      |                 ~^~~~~~~~~~~~
PHASE123CODE.cpp:1365:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1365 |         for(j=0;j<Dose.n_rows;j++){
      |                 ~^~~~~~~~~~~~
PHASE123CODE.cpp:625:7: warning: unused variable ‘Count’ [-Wunused-variable]
  625 |   int Count=0;
      |       ^~~~~
PHASE123CODE.cpp:635:7: warning: unused variable ‘nREP’ [-Wunused-variable]
  635 |   int nREP=0;
      |       ^~~~
PHASE123CODE.cpp:678:10: warning: unused variable ‘min1’ [-Wunused-variable]
  678 |   double min1=0;
      |          ^~~~
PHASE123CODE.cpp: In function ‘int AssignEffTox(arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, int)’:
PHASE123CODE.cpp:1728:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1728 |           for(j=0;j<Dose.n_rows;j++){
      |                   ~^~~~~~~~~~~~
PHASE123CODE.cpp:1773:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1773 |       for(j=0;j<Dose.n_rows;j++){
      |               ~^~~~~~~~~~~~
PHASE123CODE.cpp:1791:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1791 |       for(j=0;j<Dose.n_rows;j++){
      |               ~^~~~~~~~~~~~
PHASE123CODE.cpp:1810:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1810 |       for(j=0;j<Dose.n_rows;j++){
      |               ~^~~~~~~~~~~~
PHASE123CODE.cpp:1840:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1840 |           for(j=1;j<Dose.n_rows;j++){
      |                   ~^~~~~~~~~~~~
PHASE123CODE.cpp:1517:7: warning: unused variable ‘Count’ [-Wunused-variable]
 1517 |   int Count=0;
      |       ^~~~~
PHASE123CODE.cpp:1527:7: warning: unused variable ‘nREP’ [-Wunused-variable]
 1527 |   int nREP=0;
      |       ^~~~
PHASE123CODE.cpp:1550:7: warning: unused variable ‘m’ [-Wunused-variable]
 1550 |   int m=0;
      |       ^
PHASE123CODE.cpp:1567:7: warning: variable ‘STOPPED’ set but not used [-Wunused-but-set-variable]
 1567 |   int STOPPED=0;
      |       ^~~~~~~
PHASE123CODE.cpp:1568:7: warning: unused variable ‘i’ [-Wunused-variable]
 1568 |   int i=0;
      |       ^
PHASE123CODE.cpp:1570:10: warning: unused variable ‘min1’ [-Wunused-variable]
 1570 |   double min1=0;
      |          ^~~~
PHASE123CODE.cpp:1574:7: warning: unused variable ‘nRep’ [-Wunused-variable]
 1574 |   int nRep=0;
      |       ^~~~
PHASE123CODE.cpp: In function ‘int RandomEffTox(arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, int)’:
PHASE123CODE.cpp:2212:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2212 |       for(j=0;j<Dose.n_rows;j++){
      |               ~^~~~~~~~~~~~
PHASE123CODE.cpp:2257:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2257 |   for(j=0;j<Dose.n_rows;j++){
      |           ~^~~~~~~~~~~~
PHASE123CODE.cpp:2275:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2275 |   for(j=0;j<Dose.n_rows;j++){
      |           ~^~~~~~~~~~~~
PHASE123CODE.cpp:2294:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2294 |   for(j=0;j<Dose.n_rows;j++){
      |           ~^~~~~~~~~~~~
PHASE123CODE.cpp:2001:7: warning: unused variable ‘Count’ [-Wunused-variable]
 2001 |   int Count=0;
      |       ^~~~~
PHASE123CODE.cpp:2011:7: warning: unused variable ‘nREP’ [-Wunused-variable]
 2011 |   int nREP=0;
      |       ^~~~
PHASE123CODE.cpp:2034:7: warning: unused variable ‘m’ [-Wunused-variable]
 2034 |   int m=0;
      |       ^
PHASE123CODE.cpp:2051:7: warning: variable ‘STOPPED’ set but not used [-Wunused-but-set-variable]
 2051 |   int STOPPED=0;
      |       ^~~~~~~
PHASE123CODE.cpp:2052:7: warning: unused variable ‘i’ [-Wunused-variable]
 2052 |   int i=0;
      |       ^
PHASE123CODE.cpp:2054:10: warning: unused variable ‘min1’ [-Wunused-variable]
 2054 |   double min1=0;
      |          ^~~~
PHASE123CODE.cpp:2058:7: warning: unused variable ‘nRep’ [-Wunused-variable]
 2058 |   int nRep=0;
      |       ^~~~
PHASE123CODE.cpp: In function ‘int SampleBirth(arma::vec)’:
PHASE123CODE.cpp:2408:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2408 |   for(m=1;m<cumprob.n_rows;m++){
      |           ~^~~~~~~~~~~~~~~
PHASE123CODE.cpp:2422:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 2422 |     for(m=1;m<cumprob.n_rows;m++){
      |             ~^~~~~~~~~~~~~~~
PHASE123CODE.cpp: In function ‘Rcpp::List PieceMCMC(arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, int, arma::mat, arma::mat)’:
PHASE123CODE.cpp:2887:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
 2887 |       for(j=(Spot+1);j<(s.n_rows-1);j++){
      |                      ~^~~~~~~~~~~~~
PHASE123CODE.cpp:2894:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
 2894 |       for(j=(Spot+2);j<(lam.n_rows-1);j++){
      |                      ~^~~~~~~~~~~~~~~
PHASE123CODE.cpp:3017:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
 3017 |         for(j=Spot;j<(lam.n_rows-1);j++){
      |                    ~^~~~~~~~~~~~~~~
PHASE123CODE.cpp:3029:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
 3029 |       for(j=Spot; j<(s.n_rows-1);j++){
      |                   ~^~~~~~~~~~~~~
PHASE123CODE.cpp:3149:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3149 |     for(j=0;j<Dose.n_rows;j++){
      |             ~^~~~~~~~~~~~
PHASE123CODE.cpp:3410:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3410 |     for(j=0;j<sstore.n_cols;j++){
      |             ~^~~~~~~~~~~~~~
PHASE123CODE.cpp:3414:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3414 |     for(j=0;j<lamstore.n_cols;j++){
      |             ~^~~~~~~~~~~~~~~~
PHASE123CODE.cpp:3418:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3418 |     for(j=0;j<Dose.n_rows;j++){
      |             ~^~~~~~~~~~~~
PHASE123CODE.cpp:2492:7: warning: unused variable ‘b’ [-Wunused-variable]
 2492 |   int b=0;
      |       ^
PHASE123CODE.cpp:2496:7: warning: unused variable ‘B1’ [-Wunused-variable]
 2496 |   int B1=B;
      |       ^~
PHASE123CODE.cpp: In function ‘arma::mat EFFTOX(arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, int)’:
PHASE123CODE.cpp:3675:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3675 |       for(j=0;j<Dose.n_rows;j++){
      |               ~^~~~~~~~~~~~
PHASE123CODE.cpp:3707:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3707 |   for(j=0;j<Dose.n_rows;j++){
      |           ~^~~~~~~~~~~~
PHASE123CODE.cpp:3718:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3718 |   for(j=0;j<Dose.n_rows;j++){
      |           ~^~~~~~~~~~~~
PHASE123CODE.cpp:3740:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 3740 |   for(j=0;j<Dose.n_rows;j++){
      |           ~^~~~~~~~~~~~
PHASE123CODE.cpp:3540:7: warning: unused variable ‘m’ [-Wunused-variable]
 3540 |   int m=0;
      |       ^
g++-13 -std=gnu++17 -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++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o Phase123.so PHASE123CODE.o RcppExports.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmp1kCnP8/R.INSTALL24d0c9944ccc/Phase123/src'
make[1]: Entering directory '/tmp/Rtmp1kCnP8/R.INSTALL24d0c9944ccc/Phase123/src'
make[1]: Leaving directory '/tmp/Rtmp1kCnP8/R.INSTALL24d0c9944ccc/Phase123/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Phase123/00new/Phase123/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘Phase123’
    finding HTML links ... done
    AssignEffTox                            html  
    EFFTOX                                  html  
    PieceMCMC                               html  
    RandomEffTox                            html  
    Reoptimize                              html  
    Reoptimize1                             html  
    ReturnMeanControl                       html  
    ReturnMeansAgent                        html  
    ReturnOCS                               html  
    RunAdaptiveEffToxTrial                  html  
    SimPhase123                             html  
    SimPhase3                               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
* creating tarball
packaged installation of ‘Phase123’ as ‘Phase123_2.1_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (Phase123)