* installing *source* package 'GENLIB' ... ** using staged installation ** applying installation-time patches can't find file to patch at input line 4 Perhaps you used the wrong -p or --strip option? The text leading up to this was: -------------------------- |diff -Nru orig/GENLIB/src/Makevars.win patched/GENLIB/src/Makevars.win |--- orig/GENLIB/src/Makevars.win 2022-02-24 05:05:45.000000000 +0100 |+++ patched/GENLIB/src/Makevars.win 2024-02-05 19:52:21.026257800 +0100 -------------------------- No file to patch. Skipping patch. 1 out of 1 hunk ignored WARNING: failed to apply patch d:/RCompile/CRANpkg/r_packages/patches/CRAN/GENLIB.diff ** libs using C compiler: 'gcc.exe (GCC) 12.3.0' using C++ compiler: 'g++.exe (GCC) 12.3.0' g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/BH/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c apparentement.cpp -o apparentement.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/BH/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c asa239.cpp -o asa239.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/BH/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c congen.cpp -o congen.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/BH/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c consanguinite.cpp -o consanguinite.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/BH/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c exception.cpp -o exception.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/BH/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:448:45: warning: 'convert_dist' may be used uninitialized [-Wmaybe-uninitialized] 448 | convert_dist(nbRecomb2, CO_arrayM, Morgan_Len[1], BP_len, bp_map_MO ,cm_map_MO, BP_CO_arrayM); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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) | ^~~~~~~~~~~~ fondateur.cpp:444:55: warning: 'SampleCO.void (Crossovers::*)(const int&, double*, double*, int&, std::mt19937&, double*)::__pfn' may be used uninitialized [-Wmaybe-uninitialized] 444 | (crossovers.*SampleCO)(2, probRecomb, Morgan_Len, nbRecomb2, my_rng, CO_arrayM); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/BH/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genphi.cpp -o genphi.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/BH/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hal.cpp -o hal.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/BH/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c interface.cpp -o interface.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/BH/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c md5.cpp -o md5.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/BH/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mpajout.c -o mpajout.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/BH/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mpi.c -o mpi.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/BH/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mplogic.c -o mplogic.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/BH/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c outilanal.cpp -o outilanal.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/BH/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 | ^~~~~~~ In function 'int SortPrioriteArbre(CIndSimul*, CIndSimul**, int*, int*, Clist**)', inlined from 'void StartSortPrioriteArbre(CIndSimul*, CIndSimul**, int*, int*)' at outils.cpp:866:22: outils.cpp:934:27: warning: storing the address of local variable 'listedebut' in 'listenoeud' [-Wdangling-pointer=] 934 | listenoeud=list; | ~~~~~~~~~~^~~~~ outils.cpp: In function 'void StartSortPrioriteArbre(CIndSimul*, CIndSimul**, int*, int*)': outils.cpp:824:16: note: 'listedebut' declared here 824 | Clist *listedebut; | ^~~~~~~~~~ outils.cpp:926:24: note: 'listenoeud' declared here 926 | static Clist **listenoeud=NULL; | ^~~~~~~~~~ g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/BH/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c probsimul.cpp -o probsimul.o gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/BH/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c registerDynamicSymbol.c -o registerDynamicSymbol.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/BH/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c statanal.cpp -o statanal.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/BH/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c userInterface.cpp -o userInterface.o g++ -std=gnu++17 -shared -s -static-libgcc -o GENLIB.dll tmp.def 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 -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR installing to d:/RCompile/CRANincoming/R-devel/lib/00LOCK-GENLIB/00new/GENLIB/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GENLIB)