Install log for 'junctions'

* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘junctions’ ...
** this is package ‘junctions’ version ‘2.1.3’
** package ‘junctions’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-8) 14.3.0’
using C++17
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp6hqOY9/R.INSTALL3c52c278cfe155/junctions/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/nloptr/include' -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/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Fish.cpp -o Fish.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/nloptr/include' -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/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Output.cpp -o Output.o
Output.cpp: In function ‘std::vector<int> detect_ancestry(const std::vector<junction>&, const std::vector<double>&)’:
Output.cpp:102:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<junction>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  102 |         for (; j <= (G.size() - 1); ++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/nloptr/include' -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/RcppParallel/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/nloptr/include' -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/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c backcrossing.cpp -o backcrossing.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/nloptr/include' -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/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c estimate_time_unphased.cpp -o estimate_time_unphased.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/nloptr/include' -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/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c main_functions.cpp -o main_functions.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/nloptr/include' -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/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c unphased.cpp -o unphased.o
unphased.cpp: In function ‘void update_pop(const std::vector<Fish_inf>&, std::vector<Fish_inf>*, int, double, size_t)’:
unphased.cpp:37:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   37 |     for (size_t i = 0; i < popSize; ++i) {
      |                        ~~^~~~~~~~~
unphased.cpp: In function ‘Output simulation_phased_nonphased(int, double, int, double, std::vector<double>, const Rcpp::NumericVector&, bool, bool, int, rnd_t*, size_t)’:
unphased.cpp:105:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  105 |   for (size_t t = 0; t <= maxTime; ++t) {
      |                      ~~^~~~~~~~~~
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o junctions.so Fish.o Output.o RcppExports.o backcrossing.o estimate_time_unphased.o main_functions.o unphased.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp6hqOY9/R.INSTALL3c52c278cfe155/junctions/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp6hqOY9/R.INSTALL3c52c278cfe155/junctions/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp6hqOY9/R.INSTALL3c52c278cfe155/junctions/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-junctions/00new/junctions/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘junctions’
    finding HTML links ... done
    calc_k                                  html  
    calculate_mat                           html  
    estimate_time                           html  
    estimate_time_diploid                   html  
    estimate_time_haploid                   html  
    estimate_time_one_chrom                 html  
    junctions-package                       html  
    log_likelihood_diploid                  html  
    log_likelihood_haploid                  html  
    number_of_junctions                     html  
    number_of_junctions_backcross           html  
    number_of_junctions_di                  html  
    number_of_junctions_markers             html  
    sim_backcrossing                        html  
    sim_fin_chrom                           html  
    sim_inf_chrom                           html  
    sim_phased_unphased                     html  
    time_error                              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 (junctions)