############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf chromDraw.buildbin-libdir && mkdir chromDraw.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chromDraw.buildbin-libdir chromDraw_2.22.0.tar.gz ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'chromDraw' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Shapes.cpp -o libBoard/src/Shapes.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Board.cpp -o libBoard/src/Board.o In file included from ./libBoard/include/board/Tools.h:102, from ./libBoard/include/board/Shapes.h:51, from ./libBoard/include/Board.h:51, from libBoard/src/Board.cpp:43: In function 'void LibBoard::secured_ctime(char*, const time_t*, size_t)', inlined from 'void LibBoard::Board::saveEPS(const char*, double, double, double) const' at libBoard/src/Board.cpp:760:18: ./libBoard/include/board/Tools.ih:27:10: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 255 equals destination size [-Wstringop-truncation] strncpy( str, ctime(t), count ); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Path.cpp -o libBoard/src/Path.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Color.cpp -o libBoard/src/Color.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o "C:/rtools40/mingw32/bin/"ar crs libSn1.a libBoard/src/Shapes.o libBoard/src/Tools.o libBoard/src/Board.o libBoard/src/Transforms.o libBoard/src/Rect.o libBoard/src/ShapeList.o libBoard/src/Path.o libBoard/src/Color.o libBoard/src/PSFonts.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/parameters.cpp -o chromDrawCPP/parameters.o chromDrawCPP/parameters.cpp:66:21: warning: extra tokens at end of #ifdef directive #ifdef _WIN32 || _WIN64 ^~ chromDrawCPP/parameters.cpp:147:15: warning: extra tokens at end of #ifdef directive #ifdef _WIN32 || _WIN64 ^~ chromDrawCPP/parameters.cpp:159:15: warning: extra tokens at end of #ifdef directive #ifdef _WIN32 || _WIN64 ^~ chromDrawCPP/parameters.cpp: In member function 'int parameters::loadArguments(int, char**)': chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "--format"}; ^ chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/ideogram.cpp -o chromDrawCPP/ideogram.o chromDrawCPP/ideogram.cpp: In member function 'int ideogram::loadMatrix(std::__cxx11::string, std::__cxx11::string)': chromDrawCPP/ideogram.cpp:80:2: warning: 'retVal' may be used uninitialized in this function [-Wmaybe-uninitialized] if(retVal != 0) ^~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/getOpts.cpp -o chromDrawCPP/getOpts.o chromDrawCPP/getOpts.cpp: In member function 'char getOpts::getOptions(int, char**, char*, char**)': chromDrawCPP/getOpts.cpp:47:8: warning: unused variable 'x' [-Wunused-variable] char x = argv[argcurent][1]; ^ chromDrawCPP/getOpts.cpp:48:8: warning: unused variable 'y' [-Wunused-variable] char y = argv[argcurent][2]; ^ chromDrawCPP/getOpts.cpp:49:8: warning: unused variable 'o' [-Wunused-variable] char o = optv[optcurent]; ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/canvas.cpp -o chromDrawCPP/canvas.o chromDrawCPP/canvas.cpp: In member function 'void canvas::lin_drawRectangleMarkSign(int, canvas::ELocationOnChromosome, int)': chromDrawCPP/canvas.cpp:320:8: warning: 'coordinate_y' may be used uninitialized in this function [-Wmaybe-uninitialized] float coordinate_y; ^~~~~~~~~~~~ chromDrawCPP/canvas.cpp: In member function 'void canvas::lin_drawEllipseMarkSign(int, canvas::ELocationOnChromosome, int)': chromDrawCPP/canvas.cpp:396:8: warning: 'coordinate_y' may be used uninitialized in this function [-Wmaybe-uninitialized] float coordinate_y; ^~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/karyotype.cpp -o chromDrawCPP/karyotype.o chromDrawCPP/karyotype.cpp: In member function 'int karyotype::loadMatrix(std::ifstream*)': chromDrawCPP/karyotype.cpp:266:14: warning: deleting object of polymorphic class type 'chBlock' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete block; ^~~~~ chromDrawCPP/karyotype.cpp:274:13: warning: deleting object of polymorphic class type 'chBlock' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete block; ^~~~~ chromDrawCPP/karyotype.cpp:315:13: warning: deleting object of polymorphic class type 'chCentromere' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete centromere; ^~~~~~~~~~ chromDrawCPP/karyotype.cpp:421:14: warning: deleting object of polymorphic class type 'markSign' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete mark; ^~~~ chromDrawCPP/karyotype.cpp:429:13: warning: deleting object of polymorphic class type 'markSign' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete mark; ^~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o "C:/rtools40/mingw32/bin/"ar crs libSn2.a chromDrawCPP/chromosomeMark.o chromDrawCPP/chromosomeElement.o chromDrawCPP/parameters.o chromDrawCPP/colorPalette.o chromDrawCPP/chromosomeSign.o chromDrawCPP/ideogram.o chromDrawCPP/chBlock.o chromDrawCPP/getOpts.o chromDrawCPP/markSign.o chromDrawCPP/chromosome.o chromDrawCPP/canvas.o chromDrawCPP/color.o chromDrawCPP/karyotype.o chromDrawCPP/chCentromere.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDraw.cpp -o chromDraw.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_chromDraw.cpp -o R_init_chromDraw.o "C:/rtools40/mingw32/bin/"ar crs libSn3.a RcppExports.o chromDraw.o R_init_chromDraw.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o chromDraw.dll tmp.def chromDraw.o RcppExports.o libSn1.a libSn2.a libSn3.a -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/chromDraw.buildbin-libdir/00LOCK-chromDraw/00new/chromDraw/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'chromDraw' finding HTML links ... done chromDraw-package html chromDraw html chromDrawGR html convertInputColors html convertInputData html main_chromDraw html ** 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 install for x64 * installing *source* package 'chromDraw' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Shapes.cpp -o libBoard/src/Shapes.o In file included from ./libBoard/include/board/Rect.h:46, from libBoard/src/Shapes.cpp:42: ./libBoard/include/board/Point.h: In member function 'virtual LibBoard::Ellipse& LibBoard::Ellipse::rotate(double, const LibBoard::Point&)': ./libBoard/include/board/Point.h:71:40: warning: '' is used uninitialized in this function [-Wuninitialized] Point( const Point & other ):x(other.x),y(other.y) { } ~~~~~~^ ./libBoard/include/board/Point.h:71:51: warning: '*((void*)& +8)' is used uninitialized in this function [-Wuninitialized] Point( const Point & other ):x(other.x),y(other.y) { } ~~~~~~^ ./libBoard/include/board/Point.h:71:40: warning: '' is used uninitialized in this function [-Wuninitialized] Point( const Point & other ):x(other.x),y(other.y) { } ~~~~~~^ ./libBoard/include/board/Point.h:71:51: warning: '*((void*)& +8)' is used uninitialized in this function [-Wuninitialized] Point( const Point & other ):x(other.x),y(other.y) { } ~~~~~~^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Board.cpp -o libBoard/src/Board.o In file included from ./libBoard/include/board/Tools.h:102, from ./libBoard/include/board/Shapes.h:51, from ./libBoard/include/Board.h:51, from libBoard/src/Board.cpp:43: In function 'void LibBoard::secured_ctime(char*, const time_t*, size_t)', inlined from 'void LibBoard::Board::saveEPS(const char*, double, double, double) const' at libBoard/src/Board.cpp:760:18: ./libBoard/include/board/Tools.ih:27:10: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 255 equals destination size [-Wstringop-truncation] strncpy( str, ctime(t), count ); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Path.cpp -o libBoard/src/Path.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Color.cpp -o libBoard/src/Color.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o "C:/rtools40/mingw64/bin/"ar crs libSn1.a libBoard/src/Shapes.o libBoard/src/Tools.o libBoard/src/Board.o libBoard/src/Transforms.o libBoard/src/Rect.o libBoard/src/ShapeList.o libBoard/src/Path.o libBoard/src/Color.o libBoard/src/PSFonts.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/parameters.cpp -o chromDrawCPP/parameters.o chromDrawCPP/parameters.cpp:66:21: warning: extra tokens at end of #ifdef directive #ifdef _WIN32 || _WIN64 ^~ chromDrawCPP/parameters.cpp:147:15: warning: extra tokens at end of #ifdef directive #ifdef _WIN32 || _WIN64 ^~ chromDrawCPP/parameters.cpp:159:15: warning: extra tokens at end of #ifdef directive #ifdef _WIN32 || _WIN64 ^~ chromDrawCPP/parameters.cpp: In member function 'int parameters::loadArguments(int, char**)': chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "--format"}; ^ chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/ideogram.cpp -o chromDrawCPP/ideogram.o chromDrawCPP/ideogram.cpp: In member function 'int ideogram::loadMatrix(std::__cxx11::string, std::__cxx11::string)': chromDrawCPP/ideogram.cpp:80:2: warning: 'retVal' may be used uninitialized in this function [-Wmaybe-uninitialized] if(retVal != 0) ^~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/getOpts.cpp -o chromDrawCPP/getOpts.o chromDrawCPP/getOpts.cpp: In member function 'char getOpts::getOptions(int, char**, char*, char**)': chromDrawCPP/getOpts.cpp:47:8: warning: unused variable 'x' [-Wunused-variable] char x = argv[argcurent][1]; ^ chromDrawCPP/getOpts.cpp:48:8: warning: unused variable 'y' [-Wunused-variable] char y = argv[argcurent][2]; ^ chromDrawCPP/getOpts.cpp:49:8: warning: unused variable 'o' [-Wunused-variable] char o = optv[optcurent]; ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/canvas.cpp -o chromDrawCPP/canvas.o chromDrawCPP/canvas.cpp: In member function 'void canvas::lin_drawRectangleMarkSign(int, canvas::ELocationOnChromosome, int)': chromDrawCPP/canvas.cpp:320:8: warning: 'coordinate_y' may be used uninitialized in this function [-Wmaybe-uninitialized] float coordinate_y; ^~~~~~~~~~~~ chromDrawCPP/canvas.cpp: In member function 'void canvas::lin_drawEllipseMarkSign(int, canvas::ELocationOnChromosome, int)': chromDrawCPP/canvas.cpp:396:8: warning: 'coordinate_y' may be used uninitialized in this function [-Wmaybe-uninitialized] float coordinate_y; ^~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/karyotype.cpp -o chromDrawCPP/karyotype.o chromDrawCPP/karyotype.cpp: In member function 'int karyotype::loadMatrix(std::ifstream*)': chromDrawCPP/karyotype.cpp:266:14: warning: deleting object of polymorphic class type 'chBlock' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete block; ^~~~~ chromDrawCPP/karyotype.cpp:274:13: warning: deleting object of polymorphic class type 'chBlock' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete block; ^~~~~ chromDrawCPP/karyotype.cpp:315:13: warning: deleting object of polymorphic class type 'chCentromere' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete centromere; ^~~~~~~~~~ chromDrawCPP/karyotype.cpp:421:14: warning: deleting object of polymorphic class type 'markSign' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete mark; ^~~~ chromDrawCPP/karyotype.cpp:429:13: warning: deleting object of polymorphic class type 'markSign' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete mark; ^~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o "C:/rtools40/mingw64/bin/"ar crs libSn2.a chromDrawCPP/chromosomeMark.o chromDrawCPP/chromosomeElement.o chromDrawCPP/parameters.o chromDrawCPP/colorPalette.o chromDrawCPP/chromosomeSign.o chromDrawCPP/ideogram.o chromDrawCPP/chBlock.o chromDrawCPP/getOpts.o chromDrawCPP/markSign.o chromDrawCPP/chromosome.o chromDrawCPP/canvas.o chromDrawCPP/color.o chromDrawCPP/karyotype.o chromDrawCPP/chCentromere.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDraw.cpp -o chromDraw.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_chromDraw.cpp -o R_init_chromDraw.o "C:/rtools40/mingw64/bin/"ar crs libSn3.a RcppExports.o chromDraw.o R_init_chromDraw.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o chromDraw.dll tmp.def chromDraw.o RcppExports.o libSn1.a libSn2.a libSn3.a -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/chromDraw.buildbin-libdir/chromDraw/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'chromDraw' as chromDraw_2.22.0.zip * DONE (chromDraw)