Install log for 'magi'

* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘magi’ ...
** package ‘magi’ 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/Rtmp9UGhpR/R.INSTALL248f6f5d80bcbc/magi/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'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DNDEBUG -I'../inst/include' -fpic  -g -O2 -Wall -pedantic -mtune=native   -c MagiMain.cpp -o MagiMain.o
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'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DNDEBUG -I'../inst/include' -fpic  -g -O2 -Wall -pedantic -mtune=native   -c MagiSolver.cpp -o MagiSolver.o
In file included from MagiSolver.cpp:3:
tgtdistr.h:4: warning: "NDEBUG" redefined
    4 | #define NDEBUG
      | 
<command-line>: note: this is the location of the previous definition
MagiSolver.cpp: In member function ‘void MagiSolver::setupPhiSigma()’:
MagiSolver.cpp:168:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  168 |             for(unsigned j = 0; j < phiDim; j++){
      |                                 ~~^~~~~~~~
MagiSolver.cpp:206:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  206 |             for(unsigned j = 0; j < phiDim; j++){
      |                                 ~~^~~~~~~~
MagiSolver.cpp:206:35: warning: ‘phiDim’ may be used uninitialized [-Wmaybe-uninitialized]
  206 |             for(unsigned j = 0; j < phiDim; j++){
      |                                 ~~^~~~~~~~
MagiSolver.cpp:185:17: note: ‘phiDim’ was declared here
  185 |             int phiDim;
      |                 ^~~~~~
MagiSolver.cpp:168:37: warning: ‘phiDim’ may be used uninitialized [-Wmaybe-uninitialized]
  168 |             for(unsigned j = 0; j < phiDim; j++){
      |                                     ^~~~~~
MagiSolver.cpp:144:17: note: ‘phiDim’ was declared here
  144 |             int phiDim;
      |                 ^~~~~~
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'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DNDEBUG -I'../inst/include' -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
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'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DNDEBUG -I'../inst/include' -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppFullloglikelihood.cpp -o RcppFullloglikelihood.o
In file included from RcppFullloglikelihood.cpp:3:
tgtdistr.h:4: warning: "NDEBUG" redefined
    4 | #define NDEBUG
      | 
<command-line>: note: this is the location of the previous definition
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'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DNDEBUG -I'../inst/include' -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppTestingUtilities.cpp -o RcppTestingUtilities.o
In file included from RcppWrapper.h:9,
                 from RcppTestingUtilities.cpp:10:
tgtdistr.h:4: warning: "NDEBUG" redefined
    4 | #define NDEBUG
      | 
<command-line>: note: this is the location of the previous definition
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'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DNDEBUG -I'../inst/include' -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppTranslation.cpp -o RcppTranslation.o
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'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DNDEBUG -I'../inst/include' -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppWrapper.cpp -o RcppWrapper.o
In file included from RcppWrapper.h:9,
                 from RcppWrapper.cpp:2:
tgtdistr.h:4: warning: "NDEBUG" redefined
    4 | #define NDEBUG
      | 
<command-line>: note: this is the location of the previous definition
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'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DNDEBUG -I'../inst/include' -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppXthetasigma.cpp -o RcppXthetasigma.o
In file included from RcppXthetasigma.cpp:3:
tgtdistr.h:4: warning: "NDEBUG" redefined
    4 | #define NDEBUG
      | 
<command-line>: note: this is the location of the previous definition
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'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DNDEBUG -I'../inst/include' -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Rcppgpsmoothing.cpp -o Rcppgpsmoothing.o
Rcppgpsmoothing.cpp:1: warning: "NDEBUG" redefined
    1 | #define NDEBUG
      | 
<command-line>: note: this is the location of the previous definition
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'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DNDEBUG -I'../inst/include' -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppsolveMagi.cpp -o RcppsolveMagi.o
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'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DNDEBUG -I'../inst/include' -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Sampler.cpp -o Sampler.o
Sampler.cpp: In member function ‘void Sampler::sampleChian(const arma::vec&, const arma::vec&, bool)’:
Sampler.cpp:19:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
   19 |     for (int t = 1; t < niter; t++){
      |                     ~~^~~~~~~
Sampler.cpp:26:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
   26 |         if (t < burnin && t > 10){
      |             ~~^~~~~~~~
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'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DNDEBUG -I'../inst/include' -fpic  -g -O2 -Wall -pedantic -mtune=native   -c band.cpp -o band.o
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'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DNDEBUG -I'../inst/include' -fpic  -g -O2 -Wall -pedantic -mtune=native   -c classDefinition.cpp -o classDefinition.o
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'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DNDEBUG -I'../inst/include' -fpic  -g -O2 -Wall -pedantic -mtune=native   -c dynamicalSystemModels.cpp -o dynamicalSystemModels.o
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'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DNDEBUG -I'../inst/include' -fpic  -g -O2 -Wall -pedantic -mtune=native   -c fullloglikelihood.cpp -o fullloglikelihood.o
In file included from fullloglikelihood.cpp:3:
tgtdistr.h:4: warning: "NDEBUG" redefined
    4 | #define NDEBUG
      | 
<command-line>: note: this is the location of the previous definition
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'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DNDEBUG -I'../inst/include' -fpic  -g -O2 -Wall -pedantic -mtune=native   -c gpcov.cpp -o gpcov.o
In file included from gpcov.cpp:3:
tgtdistr.h:4: warning: "NDEBUG" redefined
    4 | #define NDEBUG
      | 
<command-line>: note: this is the location of the previous definition
gpcov.cpp: In function ‘arma::mat mat2band(const arma::mat&, int)’:
gpcov.cpp:9:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
    9 |     for (int j = 1; j <= matInput.n_cols; j++){
      |                     ~~^~~~~~~~~~~~~~~~~~
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'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DNDEBUG -I'../inst/include' -fpic  -g -O2 -Wall -pedantic -mtune=native   -c hmc.cpp -o hmc.o
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'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DNDEBUG -I'../inst/include' -fpic  -g -O2 -Wall -pedantic -mtune=native   -c testingUtilities.cpp -o testingUtilities.o
In file included from testingUtilities.cpp:3:
tgtdistr.h:4: warning: "NDEBUG" redefined
    4 | #define NDEBUG
      | 
<command-line>: note: this is the location of the previous definition
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'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DNDEBUG -I'../inst/include' -fpic  -g -O2 -Wall -pedantic -mtune=native   -c tgtdistr.cpp -o tgtdistr.o
tgtdistr.cpp:2: warning: "NDEBUG" redefined
    2 | #define NDEBUG
      | 
<command-line>: note: this is the location of the previous definition
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'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DNDEBUG -I'../inst/include' -fpic  -g -O2 -Wall -pedantic -mtune=native   -c xthetasigma.cpp -o xthetasigma.o
In file included from xthetasigma.cpp:3:
tgtdistr.h:4: warning: "NDEBUG" redefined
    4 | #define NDEBUG
      | 
<command-line>: note: this is the location of the previous definition
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o magi.so MagiMain.o MagiSolver.o RcppExports.o RcppFullloglikelihood.o RcppTestingUtilities.o RcppTranslation.o RcppWrapper.o RcppXthetasigma.o Rcppgpsmoothing.o RcppsolveMagi.o Sampler.o band.o classDefinition.o dynamicalSystemModels.o fullloglikelihood.o gpcov.o hmc.o testingUtilities.o tgtdistr.o xthetasigma.o -llapack -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp9UGhpR/R.INSTALL248f6f5d80bcbc/magi/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp9UGhpR/R.INSTALL248f6f5d80bcbc/magi/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp9UGhpR/R.INSTALL248f6f5d80bcbc/magi/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-magi/00new/magi/libs
** R
** data
** 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 (magi)