* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘SITH’ ...
** package ‘SITH’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpM4GWM8/R.INSTALL207d9467345a05/SITH/src'
g++-14 -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 RcppExports.cpp -o RcppExports.o
g++-14 -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 gillespie.cpp -o gillespie.o
In file included from neighbors.h:10,
from gillespie.h:10,
from gillespie.cpp:1:
simutils.h: In function ‘int max_mut(std::vector<specie>&)’:
simutils.h:58:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<specie>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
58 | for(int i = 0; i < species.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~
simutils.h:59:39: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
59 | if(species[i].genotype.size() > max) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
simutils.h: In function ‘std::vector<int> bubblesort(std::vector<int>)’:
simutils.h:71:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
71 | for(int i = 0; i < a.size(); ++i) {
| ~~^~~~~~~~~~
simutils.h:72:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
72 | for(int j = i+1; j < a.size(); ++j) {
| ~~^~~~~~~~~~
gillespie.cpp: In function ‘cell birth_cellUDT(cell&, int, specie, std::vector<specie>&)’:
gillespie.cpp:243:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Edge>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
243 | for(int j = 0; j < G[*it].size(); ++j) {
| ~~^~~~~~~~~~~~~~~
gillespie.cpp: In function ‘int find_gtype(std::vector<specie>&, std::vector<int>)’:
gillespie.cpp:329:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<specie>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
329 | for(int i = 0; i < species.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~
gillespie.cpp: In function ‘bool vin(std::vector<int>, int)’:
gillespie.cpp:338:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
338 | for(int i = 0; i < v.size(); ++i) {
| ~~^~~~~~~~~~
g++-14 -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 main.cpp -o main.o
In file included from simulations.h:4,
from main.cpp:1:
simutils.h: In function ‘int max_mut(std::vector<specie>&)’:
simutils.h:58:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<specie>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
58 | for(int i = 0; i < species.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~
simutils.h:59:39: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
59 | if(species[i].genotype.size() > max) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
simutils.h: In function ‘std::vector<int> bubblesort(std::vector<int>)’:
simutils.h:71:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
71 | for(int i = 0; i < a.size(); ++i) {
| ~~^~~~~~~~~~
simutils.h:72:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
72 | for(int j = i+1; j < a.size(); ++j) {
| ~~^~~~~~~~~~
g++-14 -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 postproc.cpp -o postproc.o
In file included from postproc.h:4,
from postproc.cpp:1:
simutils.h: In function ‘int max_mut(std::vector<specie>&)’:
simutils.h:58:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<specie>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
58 | for(int i = 0; i < species.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~
simutils.h:59:39: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
59 | if(species[i].genotype.size() > max) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
simutils.h: In function ‘std::vector<int> bubblesort(std::vector<int>)’:
simutils.h:71:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
71 | for(int i = 0; i < a.size(); ++i) {
| ~~^~~~~~~~~~
simutils.h:72:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
72 | for(int j = i+1; j < a.size(); ++j) {
| ~~^~~~~~~~~~
postproc.cpp: In function ‘void PostProcessing::write_results(std::vector<cell>&, std::vector<specie>&, Rcpp::NumericMatrix&, Rcpp::IntegerMatrix&, Rcpp::IntegerVector&)’:
postproc.cpp:6:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<cell>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
6 | for(int i = 0; i < cells.size(); ++i) {
| ~~^~~~~~~~~~~~~~
postproc.cpp:17:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<specie>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17 | for(int i = 0; i < species.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~
postproc.cpp:19:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
19 | for(int j = 0; j < species[i].genotype.size(); ++j) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
postproc.cpp: In function ‘void PostProcessing::write_phylo_tree(std::vector<std::vector<int> >&, Rcpp::IntegerMatrix&)’:
postproc.cpp:31:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
31 | for(int i = 0; i < phylo_tree[0].size(); ++i) {
| ~~^~~~~~~~~~~~~~~~~~~~~~
postproc.cpp: In function ‘Rcpp::NumericMatrix PostProcessing::get_color_scheme(std::vector<specie>&)’:
postproc.cpp:42:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<specie>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
42 | for(int i = 1; i < species.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~
g++-14 -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 simulations.cpp -o simulations.o
In file included from simulations.h:4,
from simulations.cpp:1:
simutils.h: In function ‘int max_mut(std::vector<specie>&)’:
simutils.h:58:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<specie>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
58 | for(int i = 0; i < species.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~
simutils.h:59:39: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
59 | if(species[i].genotype.size() > max) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
simutils.h: In function ‘std::vector<int> bubblesort(std::vector<int>)’:
simutils.h:71:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
71 | for(int i = 0; i < a.size(); ++i) {
| ~~^~~~~~~~~~
simutils.h:72:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
72 | for(int j = i+1; j < a.size(); ++j) {
| ~~^~~~~~~~~~
simulations.cpp: In function ‘Rcpp::List Sims::simulateIA(Rcpp::List)’:
simulations.cpp:30:24: warning: comparison of integer expressions of different signedness: ‘std::vector<cell>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
30 | while(cells.size() < tumor_size)
| ~~~~~~~~~~~~~^~~~~~~~~~~~
simulations.cpp: In function ‘Rcpp::List Sims::simulateUDT(Rcpp::List)’:
simulations.cpp:105:24: warning: comparison of integer expressions of different signedness: ‘std::vector<cell>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
105 | while(cells.size() < tumor_size)
| ~~~~~~~~~~~~~^~~~~~~~~~~~
g++-14 -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 simutils.cpp -o simutils.o
In file included from simutils.cpp:1:
simutils.h: In function ‘int max_mut(std::vector<specie>&)’:
simutils.h:58:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<specie>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
58 | for(int i = 0; i < species.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~
simutils.h:59:39: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
59 | if(species[i].genotype.size() > max) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
simutils.h: In function ‘std::vector<int> bubblesort(std::vector<int>)’:
simutils.h:71:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
71 | for(int i = 0; i < a.size(); ++i) {
| ~~^~~~~~~~~~
simutils.h:72:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
72 | for(int j = i+1; j < a.size(); ++j) {
| ~~^~~~~~~~~~
simutils.cpp: In function ‘std::vector<std::vector<int> > get_perms(std::vector<int>)’:
simutils.cpp:161:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
161 | for(int i = 0; i < v.size(); ++i) {
| ~~^~~~~~~~~~
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o SITH.so RcppExports.o gillespie.o main.o postproc.o simulations.o simutils.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpM4GWM8/R.INSTALL207d9467345a05/SITH/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpM4GWM8/R.INSTALL207d9467345a05/SITH/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpM4GWM8/R.INSTALL207d9467345a05/SITH/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-SITH/00new/SITH/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘SITH’
finding HTML links ... done
SITH-package html
bulkSample html
plotSlice html
progressionChain html
progressionDAG_from_igraph html
randomBulkSamples html
randomNeedles html
randomSingleCells html
simulateTumor html
singleCell html
spatialDistribution html
visualizeTumor 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 (SITH)