Install log for 'magi'

* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘magi’ ...
** package ‘magi’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-16) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpXrlDNA/R.INSTALL3873b3755f246c/magi/src'
g++-14 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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:4:9: 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++-14 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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:4:9: warning: "NDEBUG" redefined
    4 | #define NDEBUG
      |         ^~~~~~
<command-line>: note: this is the location of the previous definition
g++-14 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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:4:9: warning: "NDEBUG" redefined
    4 | #define NDEBUG
      |         ^~~~~~
<command-line>: note: this is the location of the previous definition
g++-14 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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:4:9: warning: "NDEBUG" redefined
    4 | #define NDEBUG
      |         ^~~~~~
<command-line>: note: this is the location of the previous definition
g++-14 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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:4:9: warning: "NDEBUG" redefined
    4 | #define NDEBUG
      |         ^~~~~~
<command-line>: note: this is the location of the previous definition
g++-14 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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:1:9: warning: "NDEBUG" redefined
    1 | #define NDEBUG
      |         ^~~~~~
<command-line>: note: this is the location of the previous definition
g++-14 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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:4:9: warning: "NDEBUG" redefined
    4 | #define NDEBUG
      |         ^~~~~~
<command-line>: note: this is the location of the previous definition
g++-14 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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:4:9: 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++-14 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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:4:9: warning: "NDEBUG" redefined
    4 | #define NDEBUG
      |         ^~~~~~
<command-line>: note: this is the location of the previous definition
g++-14 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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:2:9: warning: "NDEBUG" redefined
    2 | #define NDEBUG
      |         ^~~~~~
<command-line>: note: this is the location of the previous definition
g++-14 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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:4:9: warning: "NDEBUG" redefined
    4 | #define NDEBUG
      |         ^~~~~~
<command-line>: note: this is the location of the previous definition
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpXrlDNA/R.INSTALL3873b3755f246c/magi/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpXrlDNA/R.INSTALL3873b3755f246c/magi/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpXrlDNA/R.INSTALL3873b3755f246c/magi/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-magi/00new/magi/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘magi’
    finding HTML links ... done
    FNdat                                   html  
    MagiPosterior                           html  
    MagiSolver                              html  
    calCov                                  html  
    fnmodelODE                              html  
    gpcov                                   html  
    gpmean                                  html  
    gpsmoothing                             html  
    gpsmoothllik                            html  
    hes1modelODE                            html  
    is.magioutput                           html  
    magi                                    html  
    plot.magioutput                         html  
    ptransmodelODE                          html  
    setDiscretization                       html  
    summary.magioutput                      html  
    testDynamicalModel                      html  
** 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)