############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL GeneticsPed ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'GeneticsPed' ... ** this is package 'GeneticsPed' version '1.69.0' ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.3.0' using Fortran compiler: 'GNU Fortran (GCC) 13.3.0' using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c ainverse.cc -o ainverse.o In file included from ../include/ainverse.h:20, from ainverse.cc:9: ../include/pedtemplate.h:18: warning: "R_NO_REMAP" redefined 18 | #define R_NO_REMAP | : note: this is the location of the previous definition g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c eibd.cc -o eibd.o gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c ggmatmult.f -o ggmatmult.o gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c gpi.f -o gpi.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c inbreed.cc -o inbreed.o In file included from ../include/inbreed.h:18, from inbreed.cc:10: ../include/pedtemplate.h:18: warning: "R_NO_REMAP" redefined 18 | #define R_NO_REMAP | : note: this is the location of the previous definition g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c inverseAdditive.cc -o inverseAdditive.o inverseAdditive.cc:1: warning: "R_NO_REMAP" redefined 1 | #define R_NO_REMAP | : note: this is the location of the previous definition g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c meuwissen.cc -o meuwissen.o meuwissen.cc:1: warning: "R_NO_REMAP" redefined 1 | #define R_NO_REMAP | : note: this is the location of the previous definition g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c pedSort.cc -o pedSort.o pedSort.cc:1: warning: "R_NO_REMAP" redefined 1 | #define R_NO_REMAP | : note: this is the location of the previous definition g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c pedtemplate.cc -o pedtemplate.o In file included from pedtemplate.cc:15: ../include/pedtemplate.h:18: warning: "R_NO_REMAP" redefined 18 | #define R_NO_REMAP | : note: this is the location of the previous definition pedtemplate.cc: In member function 'void Pedigree::ShowPed()': pedtemplate.cc:373:15: warning: format '%d' expects argument of type 'int', but argument 2 has type '__gnu_cxx::__normal_iterator >::difference_type' {aka 'long long int'} [-Wformat=] 373 | Rprintf("%d\t", p - pedigree.begin()); | ~^ ~~~~~~~~~~~~~~~~~~~~ | | | | int __gnu_cxx::__normal_iterator >::difference_type {aka long long int} | %lld g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c register.cc -o register.o In file included from ../include/../include/inbreed.h:18, from ../include/meuwissen.h:7, from register.cc:8: ../include/../include/pedtemplate.h:18: warning: "R_NO_REMAP" redefined 18 | #define R_NO_REMAP | : note: this is the location of the previous definition gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sargolzaei.c -o sargolzaei.o sargolzaei.c: In function 'sargolzaei': sargolzaei.c:52:32: warning: '*Ped[S][0]' may be used uninitialized [-Wmaybe-uninitialized] 52 | rPed[rN][0] = Link[Ped[S][0]]; | ~~~~~~^~~ sargolzaei.c:53:34: warning: '*Ped[D][1]' may be used uninitialized [-Wmaybe-uninitialized] 53 | rPed[rN++][1] = Link[Ped[D][1]]; | ~~~~~~^~~ sargolzaei.c:58:32: warning: '*Ped[D][0]' may be used uninitialized [-Wmaybe-uninitialized] 58 | rPed[rN][0] = Link[Ped[D][0]]; | ~~~~~~^~~ sargolzaei.c:59:34: warning: '*Ped[D][1]' may be used uninitialized [-Wmaybe-uninitialized] 59 | rPed[rN++][1] = Link[Ped[D][1]]; | ~~~~~~^~~ sargolzaei.c:72:20: warning: '*Ped[][0]' may be used uninitialized [-Wmaybe-uninitialized] 72 | if(!Ped[SId[i]][0]) | ~~~~~~~~~~~^~~ sargolzaei.c:97:26: warning: '*Ped[][0]' may be used uninitialized [-Wmaybe-uninitialized] 97 | if(S != Ped[SId[i]][0]) break; | ~~~~~~~~~~~^~~ sargolzaei.c:98:42: warning: '*Ped[][1]' may be used uninitialized [-Wmaybe-uninitialized] 98 | else F[SId[i]] = x[Link[Ped[SId[i]][1]]] * 0.5f; | ~~~~~~~~~~~^~~ g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c sortped.cc -o sortped.o In file included from sortped.cc:1: ../include/sortped.h:5: warning: "R_NO_REMAP" redefined 5 | #define R_NO_REMAP | : note: this is the location of the previous definition sortped.cc: In function 'void SortPed(Pedigree&, TPedVec&)': sortped.cc:55:5: error: 'error' was not declared in this scope; did you mean 'perror'? 55 | error("Problems in pedigree. Stopping inbreeding calculations\n"); | ^~~~~ | perror make: *** [E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:294: sortped.o] Error 1 ERROR: compilation failed for package 'GeneticsPed' * removing 'E:/biocbuild/bbs-3.21-bioc/R/library/GeneticsPed'