* installing *source* package ‘mkde’ ...
** package ‘mkde’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (GCC) 13.2.0’
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/mkde/src'
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c init.c -o init.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -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/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o mkde.so init.o mkdeFunctions.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/mkde/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/mkde/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/mkde/src'
installing to /data/gannet/ripley/R/packages/tests-devel/mkde.Rcheck/00LOCK-mkde/00new/mkde/libs
** R
** data
** 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
* DONE (mkde)