############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL Repitools ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'Repitools' ... ** this is package 'Repitools' version '1.53.0' ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 14.2.0' using C++ compiler: 'G__~1.EXE (GCC) 14.2.0' gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -D R_NO_REMAP -I. -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c const.c -o const.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -D R_NO_REMAP -I. -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c hyp2f1.c -o hyp2f1.o In file included from hyp2f1.c:81: ./mconf.h:100:9: warning: "DOMAIN" redefined 100 | #define DOMAIN 1 /* argument domain error */ | ^~~~~~ In file included from E:/biocbuild/bbs-3.21-bioc/R/include/Rmath.h:43, from hyp2f1.c:80: C:/rtools45/x86_64-w64-mingw32.static.posix/include/math.h:29:9: note: this is the location of the previous definition 29 | #define DOMAIN _DOMAIN | ^~~~~~ ./mconf.h:101:9: warning: "SING" redefined 101 | #define SING 2 /* argument singularity */ | ^~~~ C:/rtools45/x86_64-w64-mingw32.static.posix/include/math.h:30:9: note: this is the location of the previous definition 30 | #define SING _SING | ^~~~ ./mconf.h:102:9: warning: "OVERFLOW" redefined 102 | #define OVERFLOW 3 /* overflow range error */ | ^~~~~~~~ C:/rtools45/x86_64-w64-mingw32.static.posix/include/math.h:31:9: note: this is the location of the previous definition 31 | #define OVERFLOW _OVERFLOW | ^~~~~~~~ ./mconf.h:103:9: warning: "UNDERFLOW" redefined 103 | #define UNDERFLOW 4 /* underflow range error */ | ^~~~~~~~~ C:/rtools45/x86_64-w64-mingw32.static.posix/include/math.h:32:9: note: this is the location of the previous definition 32 | #define UNDERFLOW _UNDERFLOW | ^~~~~~~~~ ./mconf.h:104:9: warning: "TLOSS" redefined 104 | #define TLOSS 5 /* total loss of precision */ | ^~~~~ C:/rtools45/x86_64-w64-mingw32.static.posix/include/math.h:33:9: note: this is the location of the previous definition 33 | #define TLOSS _TLOSS | ^~~~~ ./mconf.h:105:9: warning: "PLOSS" redefined 105 | #define PLOSS 6 /* partial loss of precision */ | ^~~~~ C:/rtools45/x86_64-w64-mingw32.static.posix/include/math.h:34:9: note: this is the location of the previous definition 34 | #define PLOSS _PLOSS | ^~~~~ hyp2f1.c: In function 'hyp2f1': hyp2f1.c:126:8: warning: old-style function definition [-Wold-style-definition] 126 | double hyp2f1( a, b, c, x ) | ^~~~~~ hyp2f1.c: In function 'hyt2f1': hyp2f1.c:294:9: warning: old-style function definition [-Wold-style-definition] 294 | double hyt2f1( a, b, c, x, loss ) | ^~~~~~ hyp2f1.c: In function 'hys2f1': hyp2f1.c:438:9: warning: old-style function definition [-Wold-style-definition] 438 | double hys2f1( a, b, c, x, loss ) | ^~~~~~ g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mmeansd.cpp -o mmeansd.o mmeansd.cpp: In function 'SEXPREC* moving_mean_sd(SEXP, SEXP, SEXP)': mmeansd.cpp:33:24: warning: variable 'is' set but not used [-Wunused-but-set-variable] 33 | int * x, nval, hs, is, i; | ^~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -D R_NO_REMAP -I. -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c mtherr.c -o mtherr.o In file included from mtherr.c:58: ./mconf.h:100:9: warning: "DOMAIN" redefined 100 | #define DOMAIN 1 /* argument domain error */ | ^~~~~~ In file included from E:/biocbuild/bbs-3.21-bioc/R/include/R.h:45, from mtherr.c:56: C:/rtools45/x86_64-w64-mingw32.static.posix/include/math.h:29:9: note: this is the location of the previous definition 29 | #define DOMAIN _DOMAIN | ^~~~~~ ./mconf.h:101:9: warning: "SING" redefined 101 | #define SING 2 /* argument singularity */ | ^~~~ C:/rtools45/x86_64-w64-mingw32.static.posix/include/math.h:30:9: note: this is the location of the previous definition 30 | #define SING _SING | ^~~~ ./mconf.h:102:9: warning: "OVERFLOW" redefined 102 | #define OVERFLOW 3 /* overflow range error */ | ^~~~~~~~ C:/rtools45/x86_64-w64-mingw32.static.posix/include/math.h:31:9: note: this is the location of the previous definition 31 | #define OVERFLOW _OVERFLOW | ^~~~~~~~ ./mconf.h:103:9: warning: "UNDERFLOW" redefined 103 | #define UNDERFLOW 4 /* underflow range error */ | ^~~~~~~~~ C:/rtools45/x86_64-w64-mingw32.static.posix/include/math.h:32:9: note: this is the location of the previous definition 32 | #define UNDERFLOW _UNDERFLOW | ^~~~~~~~~ ./mconf.h:104:9: warning: "TLOSS" redefined 104 | #define TLOSS 5 /* total loss of precision */ | ^~~~~ C:/rtools45/x86_64-w64-mingw32.static.posix/include/math.h:33:9: note: this is the location of the previous definition 33 | #define TLOSS _TLOSS | ^~~~~ ./mconf.h:105:9: warning: "PLOSS" redefined 105 | #define PLOSS 6 /* partial loss of precision */ | ^~~~~ C:/rtools45/x86_64-w64-mingw32.static.posix/include/math.h:34:9: note: this is the location of the previous definition 34 | #define PLOSS _PLOSS | ^~~~~ mtherr.c: In function 'mtherr': mtherr.c:77:5: warning: old-style function definition [-Wold-style-definition] 77 | int mtherr( name, code ) | ^~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -D R_NO_REMAP -I. -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c ringo_stuff.c -o ringo_stuff.o ringo_stuff.c:13:24: warning: 'Ringo_calls' defined but not used [-Wunused-variable] 13 | static R_CallMethodDef Ringo_calls[] = { | ^~~~~~~~~~~ g++ -std=gnu++17 -shared -s -static-libgcc -o Repitools.dll tmp.def const.o hyp2f1.o mmeansd.o mtherr.o ringo_stuff.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-Repitools/00new/Repitools/libs/x64 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** 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 (Repitools)