* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘epm’ ...
** package ‘epm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/RtmpyuSoOn/R.INSTALL2f646d27f23596/epm/src'
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/RcppProgress/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/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c epm_cppFunctions.cpp -o epm_cppFunctions.o
epm_cppFunctions.cpp: In function ‘std::vector<int> intersect_int(std::vector<int>, std::vector<int>)’:
epm_cppFunctions.cpp:40:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
40 | for (int k = 0; k < vec1.size(); k++) {
| ~~^~~~~~~~~~~~~
epm_cppFunctions.cpp: In function ‘std::vector<std::__cxx11::basic_string<char> > getComponentA(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >)’:
epm_cppFunctions.cpp:77:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
77 | for (int k = 0; k < commI.size(); k++) {
| ~~^~~~~~~~~~~~~~
epm_cppFunctions.cpp: In function ‘Rcpp::List getRootToTipEdges(Rcpp::List)’:
epm_cppFunctions.cpp:143:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
143 | for (int i = 0; i < tipLabels.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
epm_cppFunctions.cpp:153:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
153 | for (int j = 0; j < nodes.size(); j++) {
| ~~^~~~~~~~~~~~~~
epm_cppFunctions.cpp: In function ‘Rcpp::NumericVector countCells(Rcpp::List, Rcpp::StringVector)’:
epm_cppFunctions.cpp:325:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
325 | for (int j = 0; j < uniqueSp.size(); j++) {
| ~~^~~~~~~~~~~~~~~~~
epm_cppFunctions.cpp: In function ‘std::vector<int> uniqueBranchesForSet(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, Rcpp::List)’:
epm_cppFunctions.cpp:423:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
423 | for (int i = 0; i < a.size(); i++) {
| ~~^~~~~~~~~~
epm_cppFunctions.cpp:428:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
428 | for (int j = 0; j < branchInd.size(); j++) {
| ~~^~~~~~~~~~~~~~~~~~
epm_cppFunctions.cpp: In function ‘Rcpp::NumericMatrix calcPairwisePhylosor2(Rcpp::List, Rcpp::List, Rcpp::String, bool)’:
epm_cppFunctions.cpp:502:59: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
502 | for (int k = 0; k < edgesCommIJ.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~~~
epm_cppFunctions.cpp:507:59: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
507 | for (int k = 0; k < edgesInotJ.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~~
epm_cppFunctions.cpp:512:59: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
512 | for (int k = 0; k < edgesJnotI.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~~
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o epm.so RcppExports.o epm_cppFunctions.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpyuSoOn/R.INSTALL2f646d27f23596/epm/src'
make[1]: Entering directory '/tmp/RtmpyuSoOn/R.INSTALL2f646d27f23596/epm/src'
make[1]: Leaving directory '/tmp/RtmpyuSoOn/R.INSTALL2f646d27f23596/epm/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-epm/00new/epm/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘epm’
finding HTML links ... done
DRstat html
addLegend html
addPhylo html
addTraits html
betadiv_disparity html
betadiv_phylogenetic html
betadiv_taxonomic html
calcMeanShape html
coordsFromEpmGrid html
createEPMgrid html
customBetaDiv html
customGridMetric html
dropSpecies html
epm-example html
epm html
epmToPhyloComm html
expandSpeciesCellList html
extractFromEpmGrid html
faithPD html
generateOccurrenceMatrix html
getExtentOfList html
getMultiMapRamp html
getSpPartialDisparities html
gridMetrics html
identify html
interactiveExtent html
plot html
plotDispersionField html
plotSpRange html
rasterToGrid html
read.epmGrid html
reduceToCommonTaxa html
singleSpCellIndex html
spCountIndex html
summarizeEpmGridList html
summary html
tableFromEpmGrid html
write.epmGrid html
writeEpmSpatial 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
* DONE (epm)