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This page was generated on 2019-10-16 12:54:46 -0400 (Wed, 16 Oct 2019).
Package 270/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
chromDraw 2.14.0 Jan Janecka
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | [ OK ] |
Package: chromDraw |
Version: 2.14.0 |
Command: rm -rf chromDraw.buildbin-libdir && mkdir chromDraw.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh chromDraw_2.14.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R chromDraw.buildbin-libdir |
StartedAt: 2019-10-16 08:20:22 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 08:21:41 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 79.2 seconds |
RetCode: 0 |
Status: OK |
PackageFile: chromDraw_2.14.0.tgz |
PackageFileSize: 1.133 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf chromDraw.buildbin-libdir && mkdir chromDraw.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh chromDraw_2.14.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R chromDraw.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=chromDraw.buildbin-libdir chromDraw_2.14.0.tar.gz' >>>>>>> * installing *source* package ‘chromDraw’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c chromDraw.cpp -o chromDraw.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c libBoard/src/Board.cpp -o libBoard/src/Board.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c libBoard/src/Color.cpp -o libBoard/src/Color.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c libBoard/src/Path.cpp -o libBoard/src/Path.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c libBoard/src/Shapes.cpp -o libBoard/src/Shapes.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -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-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-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-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-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-virtual-dtor] delete mark; ^ 5 warnings generated. clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_chromDraw.cpp -o R_init_chromDraw.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.9-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 LINKS FOR chromDraw.buildbin-libdir/chromDraw/libs//chromDraw.so >>>>>>> install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "chromDraw.buildbin-libdir/chromDraw/libs//chromDraw.so" install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "chromDraw.buildbin-libdir/chromDraw/libs//chromDraw.so" install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "chromDraw.buildbin-libdir/chromDraw/libs//chromDraw.so" install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "chromDraw.buildbin-libdir/chromDraw/libs//chromDraw.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "chromDraw.buildbin-libdir/chromDraw/libs//chromDraw.so"