* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’ * installing *source* package ‘GENLIB’ ... ** package ‘GENLIB’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-13 (Debian 13.2.0-23) 13.2.0’ using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpQDMrou/R.INSTALL195dcf50134d2f/GENLIB/src' g++-13 -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++-13 -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++-13 -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++-13 -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++-13 -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++-13 -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&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&)’: 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&, std::vector&, std::vector&, std::vector&)’: 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*, 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*); | ^~~~~~~~ fondateur.cpp:581:45: warning: ‘convert_dist’ may be used uninitialized [-Wmaybe-uninitialized] 581 | convert_dist(nbRecomb1, CO_arrayF, Morgan_Len[0], BP_len, bp_map_FA ,cm_map_FA, BP_CO_arrayF); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fondateur.cpp:407:16: note: ‘convert_dist’ was declared here 407 | void (*convert_dist)(int&, double*, const double&, const int&, int*, double*, int*); //(nbrecomb, CO_array, Morgan_len, bp_len, bp_map, cm_map, precision) | ^~~~~~~~~~~~ g++-13 -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++-13 -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++-13 -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++-13 -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-13 -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-13 -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-13 -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++-13 -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++-13 -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++-13 -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 gcc-13 -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++-13 -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++-13 -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 g++-13 -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 make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpQDMrou/R.INSTALL195dcf50134d2f/GENLIB/src' make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpQDMrou/R.INSTALL195dcf50134d2f/GENLIB/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpQDMrou/R.INSTALL195dcf50134d2f/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 * creating tarball packaged installation of ‘GENLIB’ as ‘GENLIB_1.1.10_R_x86_64-pc-linux-gnu.tar.gz’ * DONE (GENLIB)