############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL chromDraw ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'chromDraw' ... ** using staged installation ** libs g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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] 27 | strncpy( str, ctime(t), count ); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Color.cpp -o libBoard/src/Color.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Path.cpp -o libBoard/src/Path.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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: '.LibBoard::Point::x' is used uninitialized in this function [-Wuninitialized] 71 | Point( const Point & other ):x(other.x),y(other.y) { } | ~~~~~~^ ./libBoard/include/board/Point.h:71:51: warning: '.LibBoard::Point::y' is used uninitialized in this function [-Wuninitialized] 71 | Point( const Point & other ):x(other.x),y(other.y) { } | ~~~~~~^ ./libBoard/include/board/Point.h:71:40: warning: '.LibBoard::Point::x' is used uninitialized in this function [-Wuninitialized] 71 | Point( const Point & other ):x(other.x),y(other.y) { } | ~~~~~~^ ./libBoard/include/board/Point.h:71:51: warning: '.LibBoard::Point::y' is used uninitialized in this function [-Wuninitialized] 71 | Point( const Point & other ):x(other.x),y(other.y) { } | ~~~~~~^ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o ar crs libSn1.a libBoard/src/Board.o libBoard/src/Color.o libBoard/src/PSFonts.o libBoard/src/Path.o libBoard/src/Rect.o libBoard/src/ShapeList.o libBoard/src/Shapes.o libBoard/src/Tools.o libBoard/src/Transforms.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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:369:61: warning: 'coordinate_y' may be used uninitialized in this function [-Wmaybe-uninitialized] 369 | sheet.drawRectangle(last_x-0.5*sizefactor*MARK_WIDTHSIZE1, coordinate_y+0.5*sizefactor*MARK_HEIGHTSIZE1, sizefactor*MARK_WIDTHSIZE1, sizefactor*MARK_HEIGHTSIZE1); | ^~~~~~~~~~~~ chromDrawCPP/canvas.cpp: In member function 'void canvas::lin_drawEllipseMarkSign(int, canvas::ELocationOnChromosome, int)': chromDrawCPP/canvas.cpp:446:19: warning: 'coordinate_y' may be used uninitialized in this function [-Wmaybe-uninitialized] 446 | sheet.drawEllipse(last_x,coordinate_y, sizefactor*MARK_WIDTHSIZE1/2.0,sizefactor*MARK_HEIGHTSIZE1); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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] 47 | char x = argv[argcurent][1]; | ^ chromDrawCPP/getOpts.cpp:48:8: warning: unused variable 'y' [-Wunused-variable] 48 | char y = argv[argcurent][2]; | ^ chromDrawCPP/getOpts.cpp:49:8: warning: unused variable 'o' [-Wunused-variable] 49 | char o = optv[optcurent]; | ^ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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::string, std::string)': chromDrawCPP/ideogram.cpp:80:2: warning: 'retVal' may be used uninitialized in this function [-Wmaybe-uninitialized] 80 | if(retVal != 0) | ^~ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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:266:7: warning: deleting object of polymorphic class type 'chBlock' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 266 | delete block; | ^~~~~~~~~~~~ chromDrawCPP/karyotype.cpp:274:6: warning: deleting object of polymorphic class type 'chBlock' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 274 | delete block; | ^~~~~~~~~~~~ chromDrawCPP/karyotype.cpp:315:6: warning: deleting object of polymorphic class type 'chCentromere' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 315 | delete centromere; | ^~~~~~~~~~~~~~~~~ chromDrawCPP/karyotype.cpp:421:7: warning: deleting object of polymorphic class type 'markSign' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 421 | delete mark; | ^~~~~~~~~~~ chromDrawCPP/karyotype.cpp:429:6: warning: deleting object of polymorphic class type 'markSign' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 429 | delete mark; | ^~~~~~~~~~~ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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 66 | #ifdef _WIN32 || _WIN64 | ^~ chromDrawCPP/parameters.cpp:147:15: warning: extra tokens at end of #ifdef directive 147 | #ifdef _WIN32 || _WIN64 | ^~ chromDrawCPP/parameters.cpp:159:15: warning: extra tokens at end of #ifdef directive 159 | #ifdef _WIN32 || _WIN64 | ^~ chromDrawCPP/parameters.cpp: In member function 'int parameters::loadArguments(int, char**)': chromDrawCPP/parameters.cpp:42:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 42 | char *paramsExpanded[10] = {"--help", | ^~~~~~~~ chromDrawCPP/parameters.cpp:43:9: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 43 | "--outputpath", | ^~~~~~~~~~~~~~ chromDrawCPP/parameters.cpp:44:9: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 44 | "--colorinputpath", | ^~~~~~~~~~~~~~~~~~ chromDrawCPP/parameters.cpp:45:9: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 45 | "--datainputpath", | ^~~~~~~~~~~~~~~~~ chromDrawCPP/parameters.cpp:46:9: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 46 | "--scale", | ^~~~~~~~~ chromDrawCPP/parameters.cpp:47:9: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 47 | "--format"}; | ^~~~~~~~~~ ar crs libSn2.a chromDrawCPP/canvas.o chromDrawCPP/chBlock.o chromDrawCPP/chCentromere.o chromDrawCPP/chromosome.o chromDrawCPP/chromosomeElement.o chromDrawCPP/chromosomeMark.o chromDrawCPP/chromosomeSign.o chromDrawCPP/color.o chromDrawCPP/colorPalette.o chromDrawCPP/getOpts.o chromDrawCPP/ideogram.o chromDrawCPP/karyotype.o chromDrawCPP/markSign.o chromDrawCPP/parameters.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_chromDraw.cpp -o R_init_chromDraw.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDraw.cpp -o chromDraw.o ar crs libSn3.a R_init_chromDraw.o RcppExports.o chromDraw.o g++ -std=gnu++11 -shared -s -static-libgcc -o chromDraw.dll tmp.def chromDraw.o RcppExports.o libSn1.a libSn2.a libSn3.a -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-chromDraw/00new/chromDraw/libs/x64 ** R ** 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 (chromDraw)