* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘trackdem’ ...
** package ‘trackdem’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-23) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/tmp/RtmpAr28B6/R.INSTALLdbfbd7cbc062f/trackdem/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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ConnectedComponentLabelling.c -o ConnectedComponentLabelling.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -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-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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c cb.cpp -o cb.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c cb1.cpp -o cb1.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c getCoords.cpp -o getCoords.o
getCoords.cpp: In function ‘Rcpp::NumericVector getCoords(Rcpp::NumericVector, Rcpp::IntegerVector)’:
getCoords.cpp:32:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
32 | for (int k = 0; k < ind.size(); k++) {
| ~~^~~~~~~~~~~~
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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c muP.cpp -o muP.o
muP.cpp: In function ‘Rcpp::NumericVector muP(Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::IntegerVector)’:
muP.cpp:29:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
29 | for (int k = 0; k < ind.size(); k++) {
| ~~^~~~~~~~~~~~
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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c muP1.cpp -o muP1.o
muP1.cpp: In function ‘Rcpp::NumericVector muP1(Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::IntegerVector)’:
muP1.cpp:27:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
27 | for (int k = 0; k < ind.size(); k++) {
| ~~^~~~~~~~~~~~
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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c patchstats.c -o patchstats.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c sb.cpp -o sb.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c sb2.cpp -o sb2.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c sdP.cpp -o sdP.o
sdP.cpp: In function ‘Rcpp::NumericVector sdP(Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::IntegerVector)’:
sdP.cpp:31:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
31 | for (int k = 0; k < ind.size(); k++) {
| ~~^~~~~~~~~~~~
sdP.cpp:42:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
42 | for (int k = 0; k < ind.size(); k++) {
| ~~^~~~~~~~~~~~
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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c sdP1.cpp -o sdP1.o
sdP1.cpp: In function ‘Rcpp::NumericVector sdP1(Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::IntegerVector)’:
sdP1.cpp:29:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
29 | for (int k = 0; k < ind.size(); k++) {
| ~~^~~~~~~~~~~~
sdP1.cpp:36:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
36 | for (int k = 0; k < ind.size(); k++) {
| ~~^~~~~~~~~~~~
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o trackdem.so ConnectedComponentLabelling.o RcppExports.o cb.o cb1.o getCoords.o muP.o muP1.o patchstats.o sb.o sb2.o sdP.o sdP1.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpAr28B6/R.INSTALLdbfbd7cbc062f/trackdem/src'
make[1]: Entering directory '/tmp/RtmpAr28B6/R.INSTALLdbfbd7cbc062f/trackdem/src'
make[1]: Leaving directory '/tmp/RtmpAr28B6/R.INSTALLdbfbd7cbc062f/trackdem/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-trackdem/00new/trackdem/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘trackdem’
finding HTML links ... done
createBackground html
createImageSeq html
findMaxCost html
findPixelRange html
findThreshold html
identifyParticles html
loadImages html
manuallySelect html
mergeTracks html
plot.TrDm html
print.TrDm html
print.summaryTrDm html
runBatch html
simulTrajec html
subtractBackground html
summary.TrDm html
testNN html
trackParticles html
trackdem html
update.particles 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 (trackdem)