* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘rcontroll’ ...
** package ‘rcontroll’ successfully unpacked and MD5 sums checked
** using staged installation
configure: rcontroll: 0.1.0
checking whether we have a suitable tempdir... /tmp
checking for gsl-config... /usr/bin/gsl-config
configure: creating ./config.status
config.status: creating src/Makevars
--------------------------------------------------
Configuration for rcontroll 0.1.0
gsl-flags: -I/usr/include
gsl-libs: -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm
--------------------------------------------------
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/RtmpT0l3MD/R.INSTALL39a0ff713d13f7/rcontroll/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/RcppGSL/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I/usr/include -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/RcppGSL/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I/usr/include -fpic -g -O2 -Wall -pedantic -mtune=native -c troll_rcpp.cpp -o troll_rcpp.o
troll_rcpp.cpp: In function ‘std::string GetParameter(std::string&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&)’:
troll_rcpp.cpp:1169:25: 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]
1169 | while(parameter_index < parameter_names.size() && parameter_names[parameter_index] != parameter_name) parameter_index++;
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
troll_rcpp.cpp:1171:22: 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]
1171 | if(parameter_index < parameter_names.size()) parameter_value = parameter_values[parameter_index];
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
troll_rcpp.cpp: In function ‘void OutputCrownSliced(int, int, int, std::vector<float>&)’:
troll_rcpp.cpp:3413:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<float>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
3413 | for(int i = 0; i < output_statistics.size();i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~
In copy constructor ‘Species::Species(const Species&)’,
inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Species; _Args = {const Species&}; _Tp = Species]’ at /usr/include/c++/13/bits/new_allocator.h:191:4,
inlined from ‘static void std::allocator_traits<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Species; _Args = {const Species&}; _Tp = Species]’ at /usr/include/c++/13/bits/alloc_traits.h:538:17,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Species; _Alloc = std::allocator<Species>]’ at /usr/include/c++/13/bits/stl_vector.h:1283:30,
inlined from ‘void ReadInputSpecies()’ at troll_rcpp.cpp:4176:16:
troll_rcpp.cpp:558:7: warning: ‘species_dummy.Species::s_nbext’ may be used uninitialized [-Wmaybe-uninitialized]
558 | class Species {
| ^~~~~~~
troll_rcpp.cpp: In function ‘void ReadInputSpecies()’:
troll_rcpp.cpp:4175:13: note: ‘species_dummy’ declared here
4175 | Species species_dummy; // !!!: currently, species at 0 is not initialized, for legacy reasons, maybe to change
| ^~~~~~~~~~~~~
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o rcontroll.so RcppExports.o troll_rcpp.o -Wl,-O1 -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpT0l3MD/R.INSTALL39a0ff713d13f7/rcontroll/src'
make[1]: Entering directory '/tmp/RtmpT0l3MD/R.INSTALL39a0ff713d13f7/rcontroll/src'
make[1]: Leaving directory '/tmp/RtmpT0l3MD/R.INSTALL39a0ff713d13f7/rcontroll/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-rcontroll/00new/rcontroll/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 ‘rcontroll’
finding HTML links ... done
TROLL.version html
TROLLv3_climatedaytime12 html
TROLLv3_daytimevar html
TROLLv3_input html
TROLLv3_output html
TROLLv3_pointcloud html
TROLLv3_species html
autogif html
autoplot-trollsim-method html
generate_climate html
generate_lidar html
generate_parameters html
get_chm html
get_forest html
get_log html
load_output html
load_sim html
load_stack html
option.rcontroll html
pipe html
print.trollsim html
rcontroll html
stack html
troll html
trollCpp html
trollsim-class html
trollsim html
trollstack-class html
trollstack html
update_parameters html
*** copying figures
** 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 (rcontroll)