* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘mkde’ ...
** package ‘mkde’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-25) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-25) 13.2.0’
make[1]: Entering directory '/tmp/Rtmpos0pyX/R.INSTALL255c5171bfbc3a/mkde/src'
gcc-13 -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/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c init.c -o init.o
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/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c mkdeFunctions.cpp -o mkdeFunctions.o
mkdeFunctions.cpp: In function ‘SEXPREC* mkde2dGrid02(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mkdeFunctions.cpp:296:32: warning: unused variable ‘voxy’ [-Wunused-variable]
  296 |                         double voxy = yGrid[i2]; // voxel y
      |                                ^~~~
mkdeFunctions.cpp:245:20: warning: variable ‘sig2xy_inv’ set but not used [-Wunused-but-set-variable]
  245 |     double sig2xy, sig2xy_inv;
      |                    ^~~~~~~~~~
mkdeFunctions.cpp:246:23: warning: unused variable ‘xyDistSq’ [-Wunused-variable]
  246 |     double distMaxXY, xyDistSq, voxx, voxy, xyterm;
      |                       ^~~~~~~~
mkdeFunctions.cpp:246:33: warning: unused variable ‘voxx’ [-Wunused-variable]
  246 |     double distMaxXY, xyDistSq, voxx, voxy, xyterm;
      |                                 ^~~~
mkdeFunctions.cpp:246:39: warning: unused variable ‘voxy’ [-Wunused-variable]
  246 |     double distMaxXY, xyDistSq, voxx, voxy, xyterm;
      |                                       ^~~~
mkdeFunctions.cpp:246:45: warning: unused variable ‘xyterm’ [-Wunused-variable]
  246 |     double distMaxXY, xyDistSq, voxx, voxy, xyterm;
      |                                             ^~~~~~
mkdeFunctions.cpp: In function ‘SEXPREC* mkde2dGridv02interact(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mkdeFunctions.cpp:462:32: warning: unused variable ‘voxy’ [-Wunused-variable]
  462 |                         double voxy = yGrid[i2]; // voxel y
      |                                ^~~~
mkdeFunctions.cpp:394:76: warning: unused variable ‘xyDistSq’ [-Wunused-variable]
  394 |     double distMaxXY0, distMaxXY1, haloMinX, haloMaxX, haloMinY, haloMaxY, xyDistSq, xyterm, bhattaFact;
      |                                                                            ^~~~~~~~
mkdeFunctions.cpp:394:86: warning: unused variable ‘xyterm’ [-Wunused-variable]
  394 |     double distMaxXY0, distMaxXY1, haloMinX, haloMaxX, haloMinY, haloMaxY, xyDistSq, xyterm, bhattaFact;
      |                                                                                      ^~~~~~
mkdeFunctions.cpp:398:9: warning: unused variable ‘i1min’ [-Wunused-variable]
  398 |     int i1min = nX, i1max = 0, i2min = nY, i2max = 0;
      |         ^~~~~
mkdeFunctions.cpp:398:21: warning: unused variable ‘i1max’ [-Wunused-variable]
  398 |     int i1min = nX, i1max = 0, i2min = nY, i2max = 0;
      |                     ^~~~~
mkdeFunctions.cpp:398:32: warning: unused variable ‘i2min’ [-Wunused-variable]
  398 |     int i1min = nX, i1max = 0, i2min = nY, i2max = 0;
      |                                ^~~~~
mkdeFunctions.cpp:398:44: warning: unused variable ‘i2max’ [-Wunused-variable]
  398 |     int i1min = nX, i1max = 0, i2min = nY, i2max = 0;
      |                                            ^~~~~
mkdeFunctions.cpp: In function ‘SEXPREC* mkde3dGridv02(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mkdeFunctions.cpp:643:33: warning: unused variable ‘th_id’ [-Wunused-variable]
  643 |                             int th_id = omp_get_thread_num();
      |                                 ^~~~~
mkdeFunctions.cpp:631:32: warning: unused variable ‘voxy’ [-Wunused-variable]
  631 |                         double voxy = yGrid[i2]; // voxel y
      |                                ^~~~
mkdeFunctions.cpp:572:24: warning: unused variable ‘factor’ [-Wunused-variable]
  572 |     double eX, eY, eZ, factor;
      |                        ^~~~~~
mkdeFunctions.cpp:574:27: warning: unused variable ‘sig2xy_inv’ [-Wunused-variable]
  574 |     double sig2xy, sig2z, sig2xy_inv, sig2z_inv;
      |                           ^~~~~~~~~~
mkdeFunctions.cpp:574:39: warning: unused variable ‘sig2z_inv’ [-Wunused-variable]
  574 |     double sig2xy, sig2z, sig2xy_inv, sig2z_inv;
      |                                       ^~~~~~~~~
mkdeFunctions.cpp:575:33: warning: unused variable ‘xyDistSq’ [-Wunused-variable]
  575 |     double distMaxXY, distMaxZ, xyDistSq, zDistSq, tmpZ, xyterm;
      |                                 ^~~~~~~~
mkdeFunctions.cpp:575:43: warning: unused variable ‘zDistSq’ [-Wunused-variable]
  575 |     double distMaxXY, distMaxZ, xyDistSq, zDistSq, tmpZ, xyterm;
      |                                           ^~~~~~~
mkdeFunctions.cpp:575:52: warning: unused variable ‘tmpZ’ [-Wunused-variable]
  575 |     double distMaxXY, distMaxZ, xyDistSq, zDistSq, tmpZ, xyterm;
      |                                                    ^~~~
mkdeFunctions.cpp:575:58: warning: unused variable ‘xyterm’ [-Wunused-variable]
  575 |     double distMaxXY, distMaxZ, xyDistSq, zDistSq, tmpZ, xyterm;
      |                                                          ^~~~~~
mkdeFunctions.cpp:579:9: warning: unused variable ‘i1min’ [-Wunused-variable]
  579 |     int i1min = nX, i1max = 0, i2min = nY, i2max = 0, i3min = nZ, i3max = 0;
      |         ^~~~~
mkdeFunctions.cpp:579:21: warning: unused variable ‘i1max’ [-Wunused-variable]
  579 |     int i1min = nX, i1max = 0, i2min = nY, i2max = 0, i3min = nZ, i3max = 0;
      |                     ^~~~~
mkdeFunctions.cpp:579:32: warning: unused variable ‘i2min’ [-Wunused-variable]
  579 |     int i1min = nX, i1max = 0, i2min = nY, i2max = 0, i3min = nZ, i3max = 0;
      |                                ^~~~~
mkdeFunctions.cpp:579:44: warning: unused variable ‘i2max’ [-Wunused-variable]
  579 |     int i1min = nX, i1max = 0, i2min = nY, i2max = 0, i3min = nZ, i3max = 0;
      |                                            ^~~~~
mkdeFunctions.cpp:579:55: warning: unused variable ‘i3min’ [-Wunused-variable]
  579 |     int i1min = nX, i1max = 0, i2min = nY, i2max = 0, i3min = nZ, i3max = 0;
      |                                                       ^~~~~
mkdeFunctions.cpp:579:67: warning: unused variable ‘i3max’ [-Wunused-variable]
  579 |     int i1min = nX, i1max = 0, i2min = nY, i2max = 0, i3min = nZ, i3max = 0;
      |                                                                   ^~~~~
mkdeFunctions.cpp: In function ‘SEXPREC* mkde3dGridv02interact(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mkdeFunctions.cpp:869:32: warning: unused variable ‘voxy’ [-Wunused-variable]
  869 |                         double voxy = yGrid[i2]; // voxel y
      |                                ^~~~
mkdeFunctions.cpp:778:58: warning: unused variable ‘xyDistSq’ [-Wunused-variable]
  778 |     double distMaxXY0, distMaxXY1, distMaxZ0, distMaxZ1, xyDistSq, zDistSq, tmpZ, xyterm, bhattaFact;
      |                                                          ^~~~~~~~
mkdeFunctions.cpp:778:68: warning: unused variable ‘zDistSq’ [-Wunused-variable]
  778 |     double distMaxXY0, distMaxXY1, distMaxZ0, distMaxZ1, xyDistSq, zDistSq, tmpZ, xyterm, bhattaFact;
      |                                                                    ^~~~~~~
mkdeFunctions.cpp:778:77: warning: unused variable ‘tmpZ’ [-Wunused-variable]
  778 |     double distMaxXY0, distMaxXY1, distMaxZ0, distMaxZ1, xyDistSq, zDistSq, tmpZ, xyterm, bhattaFact;
      |                                                                             ^~~~
mkdeFunctions.cpp:778:83: warning: unused variable ‘xyterm’ [-Wunused-variable]
  778 |     double distMaxXY0, distMaxXY1, distMaxZ0, distMaxZ1, xyDistSq, zDistSq, tmpZ, xyterm, bhattaFact;
      |                                                                                   ^~~~~~
mkdeFunctions.cpp:780:12: warning: unused variable ‘loReflZ1’ [-Wunused-variable]
  780 |     double loReflZ1, hiReflZ1;
      |            ^~~~~~~~
mkdeFunctions.cpp:780:22: warning: unused variable ‘hiReflZ1’ [-Wunused-variable]
  780 |     double loReflZ1, hiReflZ1;
      |                      ^~~~~~~~
mkdeFunctions.cpp:784:9: warning: unused variable ‘i1min’ [-Wunused-variable]
  784 |     int i1min = nX, i1max = 0, i2min = nY, i2max = 0, i3min = nZ, i3max = 0;
      |         ^~~~~
mkdeFunctions.cpp:784:21: warning: unused variable ‘i1max’ [-Wunused-variable]
  784 |     int i1min = nX, i1max = 0, i2min = nY, i2max = 0, i3min = nZ, i3max = 0;
      |                     ^~~~~
mkdeFunctions.cpp:784:32: warning: unused variable ‘i2min’ [-Wunused-variable]
  784 |     int i1min = nX, i1max = 0, i2min = nY, i2max = 0, i3min = nZ, i3max = 0;
      |                                ^~~~~
mkdeFunctions.cpp:784:44: warning: unused variable ‘i2max’ [-Wunused-variable]
  784 |     int i1min = nX, i1max = 0, i2min = nY, i2max = 0, i3min = nZ, i3max = 0;
      |                                            ^~~~~
mkdeFunctions.cpp:784:55: warning: unused variable ‘i3min’ [-Wunused-variable]
  784 |     int i1min = nX, i1max = 0, i2min = nY, i2max = 0, i3min = nZ, i3max = 0;
      |                                                       ^~~~~
mkdeFunctions.cpp:784:67: warning: unused variable ‘i3max’ [-Wunused-variable]
  784 |     int i1min = nX, i1max = 0, i2min = nY, i2max = 0, i3min = nZ, i3max = 0;
      |                                                                   ^~~~~
mkdeFunctions.cpp: In function ‘SEXPREC* writeRasterToXDMF02(SEXP, SEXP, SEXP, SEXP, SEXP)’:
mkdeFunctions.cpp:1375:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1375 |         for (int i = 0; i < r.size(); i++) {
      |                         ~~^~~~~~~~~~
mkdeFunctions.cpp:1296:10: warning: unused variable ‘ijk’ [-Wunused-variable]
 1296 |     long ijk = 0;
      |          ^~~
mkdeFunctions.cpp: In function ‘SEXPREC* writeRasterToVTK02(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mkdeFunctions.cpp:1398:10: warning: unused variable ‘ijk’ [-Wunused-variable]
 1398 |     long ijk = 0;
      |          ^~~
mkdeFunctions.cpp:1399:12: warning: unused variable ‘xSz’ [-Wunused-variable]
 1399 |     double xSz = xGrid[1] - xGrid[0];
      |            ^~~
mkdeFunctions.cpp:1400:12: warning: unused variable ‘ySz’ [-Wunused-variable]
 1400 |     double ySz = yGrid[1] - yGrid[0];
      |            ^~~
mkdeFunctions.cpp:1401:12: warning: unused variable ‘densTmp’ [-Wunused-variable]
 1401 |     double densTmp;
      |            ^~~~~~~
mkdeFunctions.cpp: In function ‘SEXPREC* mkde2dGrid02(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mkdeFunctions.cpp:302:42: warning: ‘tOld’ may be used uninitialized [-Wmaybe-uninitialized]
  302 |                             tmpDens = (t - tOld) * pXY / 2.0;
      |                                       ~~~^~~~~~~
mkdeFunctions.cpp:242:23: note: ‘tOld’ was declared here
  242 |     double t0, t1, t, tOld, dt, alpha, totalT;
      |                       ^~~~
mkdeFunctions.cpp: In function ‘SEXPREC* mkde2dGridv02interact(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mkdeFunctions.cpp:474:42: warning: ‘tOld’ may be used uninitialized [-Wmaybe-uninitialized]
  474 |                             tmpDens = (t - tOld) * pXY / 2.0;
      |                                       ~~~^~~~~~~
mkdeFunctions.cpp:388:23: note: ‘tOld’ was declared here
  388 |     double t0, t1, t, tOld, dt, alpha;
      |                       ^~~~
mkdeFunctions.cpp: In function ‘SEXPREC* mkde3dGridv02(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mkdeFunctions.cpp:663:46: warning: ‘tOld’ may be used uninitialized [-Wmaybe-uninitialized]
  663 |                                 tmpDens = (t - tOld) * pXYZ / 2.0;
      |                                           ~~~^~~~~~~
mkdeFunctions.cpp:570:23: note: ‘tOld’ was declared here
  570 |     double t0, t1, t, tOld, dt, alpha;
      |                       ^~~~
mkdeFunctions.cpp: In function ‘SEXPREC* mkde3dGridv02interact(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mkdeFunctions.cpp:908:47: warning: ‘tOld’ may be used uninitialized [-Wmaybe-uninitialized]
  908 |                                 tmpDens0 = (t - tOld) * pXYZ0 / 2.0;
      |                                            ~~~^~~~~~~
mkdeFunctions.cpp:773:23: note: ‘tOld’ was declared here
  773 |     double t0, t1, t, tOld, dt, alpha;
      |                       ^~~~
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o mkde.so init.o mkdeFunctions.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmpos0pyX/R.INSTALL255c5171bfbc3a/mkde/src'
make[1]: Entering directory '/tmp/Rtmpos0pyX/R.INSTALL255c5171bfbc3a/mkde/src'
make[1]: Leaving directory '/tmp/Rtmpos0pyX/R.INSTALL255c5171bfbc3a/mkde/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-mkde/00new/mkde/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘mkde’
    finding HTML links ... done
    computeAreaRaster                       html  
    computeContourValues                    html  
    computeSizeMKDE                         html  
    condor                                  html  
    condordem                               html  
    condordem120                            html  
    deselectLocationsOutsideBounds          html  
    deselectNonMovementSteps                html  
    dugong                                  html  
    dugongdem                               html  
    estVarMKDE                              html  
    initializeAreaRaster                    html  
    initializeDensity                       html  
    initializeMKDE2D                        html  
    initializeMKDE3D                        html  
    initializeMovementData                  html  
    mkde-package                            html  
    mkde2Dgrid                              html  
    mkde2Dinteraction                       html  
    mkde3Dgrid                              html  
    mkde3Dinteraction                       html  
    mkdeToRaster                            html  
    panda                                   html  
    pandadem                                html  
    plotMKDE                                html  
    setMaximumZfromConstant                 html  
    setMaximumZfromRaster                   html  
    setMinimumZfromConstant                 html  
    setMinimumZfromRaster                   html  
    writeInterpolatedPathVTK                html  
    writeObservedLocationVTK                html  
    writeRasterToVTK                        html  
    writeRasterToXDMF                       html  
    writeToGRASS                            html  
    writeToVTK                              html  
    writeToXDMF                             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 ‘mkde’ as ‘mkde_0.2_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (mkde)