############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf chromDraw.buildbin-libdir && mkdir chromDraw.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh chromDraw_2.36.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R chromDraw.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=chromDraw.buildbin-libdir chromDraw_2.36.0.tar.gz' >>>>>>> * installing *source* package ‘chromDraw’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chromDraw.cpp -o chromDraw.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c libBoard/src/Board.cpp -o libBoard/src/Board.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c libBoard/src/Color.cpp -o libBoard/src/Color.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c libBoard/src/Path.cpp -o libBoard/src/Path.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c libBoard/src/Shapes.cpp -o libBoard/src/Shapes.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chromDrawCPP/canvas.cpp -o chromDrawCPP/canvas.o chromDrawCPP/canvas.cpp:362:8: warning: variable 'coordinate_y' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized] case canvas::LSouthTelomere: ^~~~~~~~~~~~~~~~~~~~~~ chromDrawCPP/canvas.cpp:369:61: note: uninitialized use occurs here 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:320:20: note: initialize the variable 'coordinate_y' to silence this warning float coordinate_y; ^ = 0.0 chromDrawCPP/canvas.cpp:438:8: warning: variable 'coordinate_y' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized] case canvas::LSouthTelomere: ^~~~~~~~~~~~~~~~~~~~~~ chromDrawCPP/canvas.cpp:446:27: note: uninitialized use occurs here sheet.drawEllipse(last_x,coordinate_y, sizefactor*MARK_WIDTHSIZE1/2.0,sizefactor*MARK_HEIGHTSIZE1); ^~~~~~~~~~~~ chromDrawCPP/canvas.cpp:396:20: note: initialize the variable 'coordinate_y' to silence this warning float coordinate_y; ^ = 0.0 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chromDrawCPP/getOpts.cpp -o chromDrawCPP/getOpts.o 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]; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chromDrawCPP/ideogram.cpp -o chromDrawCPP/ideogram.o chromDrawCPP/ideogram.cpp:76:11: warning: variable 'retVal' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (format.compare(BEDDATAFORMAT) == 0) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ chromDrawCPP/ideogram.cpp:80:5: note: uninitialized use occurs here if(retVal != 0) ^~~~~~ chromDrawCPP/ideogram.cpp:76:7: note: remove the 'if' if its condition is always true else if (format.compare(BEDDATAFORMAT) == 0) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ chromDrawCPP/ideogram.cpp:70:12: note: initialize the variable 'retVal' to silence this warning int retVal; ^ = 0 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chromDrawCPP/karyotype.cpp -o chromDrawCPP/karyotype.o chromDrawCPP/karyotype.cpp:266:7: warning: delete called on non-final 'chBlock' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete block; ^ chromDrawCPP/karyotype.cpp:274:6: warning: delete called on non-final 'chBlock' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete block; ^ chromDrawCPP/karyotype.cpp:315:6: warning: delete called on non-final 'chCentromere' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete centromere; ^ chromDrawCPP/karyotype.cpp:421:7: warning: delete called on non-final 'markSign' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete mark; ^ chromDrawCPP/karyotype.cpp:429:6: warning: delete called on non-final 'markSign' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete mark; ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chromDrawCPP/parameters.cpp -o chromDrawCPP/parameters.o chromDrawCPP/parameters.cpp:42:30: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] char *paramsExpanded[10] = {"--help", ^ chromDrawCPP/parameters.cpp:43:9: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] "--outputpath", ^ chromDrawCPP/parameters.cpp:44:9: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] "--colorinputpath", ^ chromDrawCPP/parameters.cpp:45:9: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] "--datainputpath", ^ chromDrawCPP/parameters.cpp:46:9: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] "--scale", ^ chromDrawCPP/parameters.cpp:47:9: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] "--format"}; ^ chromDrawCPP/parameters.cpp:66:21: warning: extra tokens at end of #ifdef directive [-Wextra-tokens] #ifdef _WIN32 || _WIN64 ^ // chromDrawCPP/parameters.cpp:147:15: warning: extra tokens at end of #ifdef directive [-Wextra-tokens] #ifdef _WIN32 || _WIN64 ^ // chromDrawCPP/parameters.cpp:159:15: warning: extra tokens at end of #ifdef directive [-Wextra-tokens] #ifdef _WIN32 || _WIN64 ^ // 9 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_chromDraw.cpp -o R_init_chromDraw.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/chromDraw.buildbin-libdir/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) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR chromDraw.buildbin-libdir/chromDraw/libs/chromDraw.so >>>>>>> >>>>>>> Paths before fix: chromDraw.buildbin-libdir/chromDraw/libs/chromDraw.so: chromDraw.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "chromDraw.buildbin-libdir/chromDraw/libs/chromDraw.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "chromDraw.buildbin-libdir/chromDraw/libs/chromDraw.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "chromDraw.buildbin-libdir/chromDraw/libs/chromDraw.so" >>>>>>> Paths after fix: chromDraw.buildbin-libdir/chromDraw/libs/chromDraw.so: chromDraw.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)