############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL chromDraw ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘chromDraw’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDraw.cpp -o chromDraw.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c libBoard/src/Board.cpp -o libBoard/src/Board.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c libBoard/src/Color.cpp -o libBoard/src/Color.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c libBoard/src/Path.cpp -o libBoard/src/Path.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -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: In copy constructor ‘LibBoard::Point::Point(const LibBoard::Point&)’, inlined from ‘virtual LibBoard::Ellipse& LibBoard::Ellipse::rotate(double, const LibBoard::Point&)’ at libBoard/src/Shapes.cpp:725:39: ./libBoard/include/board/Point.h:71:40: warning: using a dangling pointer to an unnamed temporary [-Wdangling-pointer=] 71 | Point( const Point & other ):x(other.x),y(other.y) { } | ~~~~~~^ ./libBoard/include/board/Point.h: In member function ‘virtual LibBoard::Ellipse& LibBoard::Ellipse::rotate(double, const LibBoard::Point&)’: ./libBoard/include/board/Point.h:238:21: note: unnamed temporary defined here 238 | return Point(*this).rotate( angle, center ); | ^ In copy constructor ‘LibBoard::Point::Point(const LibBoard::Point&)’, inlined from ‘virtual LibBoard::Ellipse& LibBoard::Ellipse::rotate(double, const LibBoard::Point&)’ at libBoard/src/Shapes.cpp:725:39: ./libBoard/include/board/Point.h:71:51: warning: using a dangling pointer to an unnamed temporary [-Wdangling-pointer=] 71 | Point( const Point & other ):x(other.x),y(other.y) { } | ~~~~~~^ ./libBoard/include/board/Point.h: In member function ‘virtual LibBoard::Ellipse& LibBoard::Ellipse::rotate(double, const LibBoard::Point&)’: ./libBoard/include/board/Point.h:238:21: note: unnamed temporary defined here 238 | return Point(*this).rotate( angle, center ); | ^ In copy constructor ‘LibBoard::Point::Point(const LibBoard::Point&)’, inlined from ‘virtual LibBoard::Ellipse& LibBoard::Ellipse::rotate(double, const LibBoard::Point&)’ at libBoard/src/Shapes.cpp:724:39: ./libBoard/include/board/Point.h:71:40: warning: using a dangling pointer to an unnamed temporary [-Wdangling-pointer=] 71 | Point( const Point & other ):x(other.x),y(other.y) { } | ~~~~~~^ ./libBoard/include/board/Point.h: In member function ‘virtual LibBoard::Ellipse& LibBoard::Ellipse::rotate(double, const LibBoard::Point&)’: ./libBoard/include/board/Point.h:238:21: note: unnamed temporary defined here 238 | return Point(*this).rotate( angle, center ); | ^ In copy constructor ‘LibBoard::Point::Point(const LibBoard::Point&)’, inlined from ‘virtual LibBoard::Ellipse& LibBoard::Ellipse::rotate(double, const LibBoard::Point&)’ at libBoard/src/Shapes.cpp:724:39: ./libBoard/include/board/Point.h:71:51: warning: using a dangling pointer to an unnamed temporary [-Wdangling-pointer=] 71 | Point( const Point & other ):x(other.x),y(other.y) { } | ~~~~~~^ ./libBoard/include/board/Point.h: In member function ‘virtual LibBoard::Ellipse& LibBoard::Ellipse::rotate(double, const LibBoard::Point&)’: ./libBoard/include/board/Point.h:238:21: note: unnamed temporary defined here 238 | return Point(*this).rotate( angle, center ); | ^ In copy constructor ‘LibBoard::Point::Point(const LibBoard::Point&)’, inlined from ‘virtual LibBoard::Ellipse& LibBoard::Ellipse::rotate(double, const LibBoard::Point&)’ at libBoard/src/Shapes.cpp:724:39: ./libBoard/include/board/Point.h:71:40: warning: ‘*(const __vector(2) double*)((char*)& + offsetof(LibBoard::Point, LibBoard::Point::x))’ is used uninitialized [-Wuninitialized] 71 | Point( const Point & other ):x(other.x),y(other.y) { } | ~~~~~~^ ./libBoard/include/board/Point.h: In member function ‘virtual LibBoard::Ellipse& LibBoard::Ellipse::rotate(double, const LibBoard::Point&)’: ./libBoard/include/board/Point.h:238:21: note: ‘’ declared here 238 | return Point(*this).rotate( angle, center ); | ^ In copy constructor ‘LibBoard::Point::Point(const LibBoard::Point&)’, inlined from ‘virtual LibBoard::Ellipse& LibBoard::Ellipse::rotate(double, const LibBoard::Point&)’ at libBoard/src/Shapes.cpp:725:39: ./libBoard/include/board/Point.h:71:40: warning: ‘.LibBoard::Point::x’ is used uninitialized [-Wuninitialized] 71 | Point( const Point & other ):x(other.x),y(other.y) { } | ~~~~~~^ ./libBoard/include/board/Point.h: In member function ‘virtual LibBoard::Ellipse& LibBoard::Ellipse::rotate(double, const LibBoard::Point&)’: ./libBoard/include/board/Point.h:238:21: note: ‘’ declared here 238 | return Point(*this).rotate( angle, center ); | ^ In copy constructor ‘LibBoard::Point::Point(const LibBoard::Point&)’, inlined from ‘virtual LibBoard::Ellipse& LibBoard::Ellipse::rotate(double, const LibBoard::Point&)’ at libBoard/src/Shapes.cpp:725:39: ./libBoard/include/board/Point.h:71:51: warning: ‘.LibBoard::Point::y’ is used uninitialized [-Wuninitialized] 71 | Point( const Point & other ):x(other.x),y(other.y) { } | ~~~~~~^ ./libBoard/include/board/Point.h: In member function ‘virtual LibBoard::Ellipse& LibBoard::Ellipse::rotate(double, const LibBoard::Point&)’: ./libBoard/include/board/Point.h:238:21: note: ‘’ declared here 238 | return Point(*this).rotate( angle, center ); | ^ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/canvas.cpp -o chromDrawCPP/canvas.o chromDrawCPP/canvas.cpp: In member function ‘void canvas::lin_drawRectangleMarkSign(int, ELocationOnChromosome, int)’: chromDrawCPP/canvas.cpp:369:68: warning: ‘coordinate_y’ may be used uninitialized [-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:320:15: note: ‘coordinate_y’ was declared here 320 | float coordinate_y; | ^~~~~~~~~~~~ chromDrawCPP/canvas.cpp: In member function ‘void canvas::lin_drawEllipseMarkSign(int, ELocationOnChromosome, int)’: chromDrawCPP/canvas.cpp:446:26: warning: ‘coordinate_y’ may be used uninitialized [-Wmaybe-uninitialized] 446 | sheet.drawEllipse(last_x,coordinate_y, sizefactor*MARK_WIDTHSIZE1/2.0,sizefactor*MARK_HEIGHTSIZE1); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ chromDrawCPP/canvas.cpp:396:15: note: ‘coordinate_y’ was declared here 396 | float coordinate_y; | ^~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/getOpts.cpp -o chromDrawCPP/getOpts.o chromDrawCPP/getOpts.cpp: In member function ‘char getOpts::getOptions(int, char**, char*, char**)’: chromDrawCPP/getOpts.cpp:47:22: warning: unused variable ‘x’ [-Wunused-variable] 47 | char x = argv[argcurent][1]; | ^ chromDrawCPP/getOpts.cpp:48:22: warning: unused variable ‘y’ [-Wunused-variable] 48 | char y = argv[argcurent][2]; | ^ chromDrawCPP/getOpts.cpp:49:22: warning: unused variable ‘o’ [-Wunused-variable] 49 | char o = optv[optcurent]; | ^ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/ideogram.cpp -o chromDrawCPP/ideogram.o chromDrawCPP/ideogram.cpp: In member function ‘int ideogram::loadMatrix(std::string, std::string)’: chromDrawCPP/ideogram.cpp:80:9: warning: ‘retVal’ may be used uninitialized [-Wmaybe-uninitialized] 80 | if(retVal != 0) | ^~ chromDrawCPP/ideogram.cpp:70:13: note: ‘retVal’ was declared here 70 | int retVal; | ^~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/karyotype.cpp -o chromDrawCPP/karyotype.o chromDrawCPP/karyotype.cpp: In member function ‘int karyotype::loadMatrix(std::ifstream*)’: chromDrawCPP/karyotype.cpp:266:49: 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:274:41: 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:315:41: 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:421:49: 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:429:41: 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++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/parameters.cpp -o chromDrawCPP/parameters.o chromDrawCPP/parameters.cpp:66:63: 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:42:37: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 42 | char *paramsExpanded[10] = {"--help", | ^~~~~~~~ chromDrawCPP/parameters.cpp:43:65: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 43 | "--outputpath", | ^~~~~~~~~~~~~~ chromDrawCPP/parameters.cpp:44:65: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 44 | "--colorinputpath", | ^~~~~~~~~~~~~~~~~~ chromDrawCPP/parameters.cpp:45:65: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 45 | "--datainputpath", | ^~~~~~~~~~~~~~~~~ chromDrawCPP/parameters.cpp:46:65: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 46 | "--scale", | ^~~~~~~~~ chromDrawCPP/parameters.cpp:47:65: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 47 | "--format"}; | ^~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_chromDraw.cpp -o R_init_chromDraw.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o chromDraw.so chromDraw.o RcppExports.o ./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 ./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 ./R_init_chromDraw.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-chromDraw/00new/chromDraw/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (chromDraw)