* installing to library ‘/home/hornik/tmp/R.check/r-devel-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 13.2.0-23) 13.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpRA6ovL/R.INSTALL19e462724495df/Phase123/src'
g++-13 -std=gnu++17 -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 PHASE123CODE.cpp -o PHASE123CODE.o
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:26,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
                 from PHASE123CODE.cpp:5:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: ‘#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed’
  321 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |                                                                                      ^
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: ‘#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead’
  326 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |                                                                           ^
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: ‘#pragma message: INFO: see the documentation for details’
  329 |   #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-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++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o Phase123.so PHASE123CODE.o RcppExports.o -llapack -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpRA6ovL/R.INSTALL19e462724495df/Phase123/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpRA6ovL/R.INSTALL19e462724495df/Phase123/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpRA6ovL/R.INSTALL19e462724495df/Phase123/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-Phase123/00new/Phase123/libs
** R
** 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 ‘Phase123’ as ‘Phase123_2.1_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (Phase123)