############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL chromDraw ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘chromDraw’ ... ** this is package ‘chromDraw’ version ‘2.37.0’ ** 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-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c chromDraw.cpp -o chromDraw.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c libBoard/src/Board.cpp -o libBoard/src/Board.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c libBoard/src/Color.cpp -o libBoard/src/Color.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c libBoard/src/Path.cpp -o libBoard/src/Path.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c libBoard/src/Shapes.cpp -o libBoard/src/Shapes.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c chromDrawCPP/canvas.cpp -o chromDrawCPP/canvas.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c chromDrawCPP/getOpts.cpp -o chromDrawCPP/getOpts.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c chromDrawCPP/ideogram.cpp -o chromDrawCPP/ideogram.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c chromDrawCPP/karyotype.cpp -o chromDrawCPP/karyotype.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -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-3.21-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c R_init_chromDraw.cpp -o R_init_chromDraw.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-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-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-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)