* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘GENLIB’ ...
** this is package ‘GENLIB’ version ‘1.1.10’
** package ‘GENLIB’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-15 (Debian 15.2.0-9) 15.2.0’
using C++ compiler: ‘g++-15 (Debian 15.2.0-9) 15.2.0’
make[1]: Entering directory '/tmp/Rtmp7PurO5/R.INSTALL2725195290bf1f/GENLIB/src'
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c apparentement.cpp -o apparentement.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c asa239.cpp -o asa239.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c congen.cpp -o congen.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c consanguinite.cpp -o consanguinite.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c exception.cpp -o exception.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fondateur.cpp -o fondateur.o
fondateur.cpp: In function ‘int simulhaplo_traceback(std::string&, std::string&, int&, int&, std::vector<int>&, std::vector<int>&, std::vector<int>&, std::vector<int>&, std::vector<int>&, std::vector<int>&)’:
fondateur.cpp:1086:9: warning: unused variable ‘numSim2’ [-Wunused-variable]
1086 | int numSim2 = std::stoi(line.substr(0,tokenPos));
| ^~~~~~~
fondateur.cpp: In function ‘void simulhaplo_compare_IBD(const int&, const int&, const int&, std::string&, std::vector<int>&, std::vector<int>&, std::vector<double>&, std::vector<int>&)’:
fondateur.cpp:1425:16: warning: unused variable ‘SimNo’ [-Wunused-variable]
1425 | int ProID, SimNo;
| ^~~~~
fondateur.cpp: In function ‘void simulhaplo(int*, int*, int, int*, int, int, double*, double*, int, int, int, double*, double*, int*, int*, std::unordered_map<int, haplotype*>*, std::string, int, int)’:
fondateur.cpp:577:55: warning: ‘SampleCO.void (Crossovers::*)(const int&, double*, double*, int&, std::mt19937&, double*)::__pfn’ may be used uninitialized [-Wmaybe-uninitialized]
577 | (crossovers.*SampleCO)(1, probRecomb, Morgan_Len, nbRecomb1, my_rng, CO_arrayF);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fondateur.cpp:398:28: note: ‘SampleCO.void (Crossovers::*)(const int&, double*, double*, int&, std::mt19937&, double*)::__pfn’ was declared here
398 | void (Crossovers::*SampleCO)(const int&, double*, double*, int&, std::mt19937&, double*);
| ^~~~~~~~
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c genphi.cpp -o genphi.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c hal.cpp -o hal.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c interface.cpp -o interface.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c md5.cpp -o md5.o
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mpajout.c -o mpajout.o
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mpi.c -o mpi.o
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mplogic.c -o mplogic.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c outilanal.cpp -o outilanal.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c outils.cpp -o outils.o
outils.cpp: In function ‘int CreerGenealogie(int*, int*, int*, int*, int, int*)’:
outils.cpp:1780:13: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation]
1780 | else
| ^~~~
outils.cpp:1783:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’
1783 | saveptr[curseur++]=Ordre[i]->sex; //Sexe de l'individu
| ^~~~~~~
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c probsimul.cpp -o probsimul.o
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/RcppCommon.h:30,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp.h:27,
from probsimul.cpp:33:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/r/check_r_headers.h:27:21: note: ‘#pragma message: R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410’
27 | #pragma message "R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c statanal.cpp -o statanal.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c userInterface.cpp -o userInterface.o
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o GENLIB.so apparentement.o asa239.o congen.o consanguinite.o exception.o fondateur.o genphi.o hal.o interface.o md5.o mpajout.o mpi.o mplogic.o outilanal.o outils.o probsimul.o registerDynamicSymbol.o statanal.o userInterface.o -rdynamic -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/tmp/Rtmp7PurO5/R.INSTALL2725195290bf1f/GENLIB/src'
make[1]: Entering directory '/tmp/Rtmp7PurO5/R.INSTALL2725195290bf1f/GENLIB/src'
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/tmp/Rtmp7PurO5/R.INSTALL2725195290bf1f/GENLIB/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-GENLIB/00new/GENLIB/libs
** R
** data
** byte-compile and prepare package for lazy loading
Creating a generic function from function ‘Dim’ in package ‘GENLIB’
** help
*** installing help indices
** 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 (GENLIB)