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BUILD BIN report for chromDraw on tokay2

This page was generated on 2019-10-16 12:32:11 -0400 (Wed, 16 Oct 2019).

Package 270/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromDraw 2.14.0
Jan Janecka
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/chromDraw
Branch: RELEASE_3_9
Last Commit: 215d8eb
Last Changed Date: 2019-05-02 11:53:52 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: chromDraw
Version: 2.14.0
Command: rm -rf chromDraw.buildbin-libdir && mkdir chromDraw.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chromDraw.buildbin-libdir chromDraw_2.14.0.tar.gz
StartedAt: 2019-10-16 08:54:06 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 08:55:36 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 89.4 seconds
RetCode: 0
Status:  OK  
PackageFile: chromDraw_2.14.0.zip
PackageFileSize: 1.681 MiB

Command output

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###
### Running command:
###
###   rm -rf chromDraw.buildbin-libdir && mkdir chromDraw.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chromDraw.buildbin-libdir chromDraw_2.14.0.tar.gz
###
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install for i386

* installing *source* package 'chromDraw' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c libBoard/src/Board.cpp -o libBoard/src/Board.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c libBoard/src/Color.cpp -o libBoard/src/Color.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c libBoard/src/Path.cpp -o libBoard/src/Path.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c libBoard/src/Shapes.cpp -o libBoard/src/Shapes.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o
C:/Rtools/mingw_32/bin/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
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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:320:8: warning: 'coordinate_y' may be used uninitialized in this function [-Wmaybe-uninitialized]
  float coordinate_y;
        ^
chromDrawCPP/canvas.cpp: In member function 'void canvas::lin_drawEllipseMarkSign(int, canvas::ELocationOnChromosome, int)':
chromDrawCPP/canvas.cpp:396:8: warning: 'coordinate_y' may be used uninitialized in this function [-Wmaybe-uninitialized]
  float coordinate_y;
        ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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]
   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];
        ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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]
  if(retVal != 0)
  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/karyotype.cpp -o chromDrawCPP/karyotype.o
chromDrawCPP/karyotype.cpp: In member function 'int karyotype::loadMatrix(std::ifstream*)':
chromDrawCPP/karyotype.cpp:266:14: warning: deleting object of polymorphic class type 'chBlock' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
       delete block;
              ^
chromDrawCPP/karyotype.cpp:274:13: warning: deleting object of polymorphic class type 'chBlock' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
      delete block;
             ^
chromDrawCPP/karyotype.cpp:315:13: warning: deleting object of polymorphic class type 'chCentromere' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
      delete centromere;
             ^
chromDrawCPP/karyotype.cpp:421:14: warning: deleting object of polymorphic class type 'markSign' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
       delete mark;
              ^
chromDrawCPP/karyotype.cpp:429:13: warning: deleting object of polymorphic class type 'markSign' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
      delete mark;
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/parameters.cpp -o chromDrawCPP/parameters.o
chromDrawCPP/parameters.cpp:66:21: warning: extra tokens at end of #ifdef directive
       #ifdef _WIN32 || _WIN64
                     ^
chromDrawCPP/parameters.cpp:147:15: warning: extra tokens at end of #ifdef directive
 #ifdef _WIN32 || _WIN64
               ^
chromDrawCPP/parameters.cpp:159:15: warning: extra tokens at end of #ifdef directive
 #ifdef _WIN32 || _WIN64
               ^
chromDrawCPP/parameters.cpp: In member function 'int parameters::loadArguments(int, char**)':
chromDrawCPP/parameters.cpp:47:19: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         "--format"};
                   ^
chromDrawCPP/parameters.cpp:47:19: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
chromDrawCPP/parameters.cpp:47:19: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
chromDrawCPP/parameters.cpp:47:19: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
chromDrawCPP/parameters.cpp:47:19: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
chromDrawCPP/parameters.cpp:47:19: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
C:/Rtools/mingw_32/bin/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
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_init_chromDraw.cpp -o R_init_chromDraw.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDraw.cpp -o chromDraw.o
C:/Rtools/mingw_32/bin/ar crs libSn3.a R_init_chromDraw.o RcppExports.o chromDraw.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o chromDraw.dll tmp.def chromDraw.o RcppExports.o libSn1.a libSn2.a libSn3.a -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/chromDraw.buildbin-libdir/00LOCK-chromDraw/00new/chromDraw/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'chromDraw'
    finding HTML links ... done
    chromDraw-package                       html  
    chromDraw                               html  
    chromDrawGR                             html  
    convertInputColors                      html  
    convertInputData                        html  
    main_chromDraw                          html  
** 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

install for x64

* installing *source* package 'chromDraw' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c libBoard/src/Board.cpp -o libBoard/src/Board.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c libBoard/src/Color.cpp -o libBoard/src/Color.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c libBoard/src/Path.cpp -o libBoard/src/Path.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c libBoard/src/Shapes.cpp -o libBoard/src/Shapes.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o
C:/Rtools/mingw_64/bin/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
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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:320:8: warning: 'coordinate_y' may be used uninitialized in this function [-Wmaybe-uninitialized]
  float coordinate_y;
        ^
chromDrawCPP/canvas.cpp: In member function 'void canvas::lin_drawEllipseMarkSign(int, canvas::ELocationOnChromosome, int)':
chromDrawCPP/canvas.cpp:396:8: warning: 'coordinate_y' may be used uninitialized in this function [-Wmaybe-uninitialized]
  float coordinate_y;
        ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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]
   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];
        ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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]
  if(retVal != 0)
  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/karyotype.cpp -o chromDrawCPP/karyotype.o
chromDrawCPP/karyotype.cpp: In member function 'int karyotype::loadMatrix(std::ifstream*)':
chromDrawCPP/karyotype.cpp:266:14: warning: deleting object of polymorphic class type 'chBlock' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
       delete block;
              ^
chromDrawCPP/karyotype.cpp:274:13: warning: deleting object of polymorphic class type 'chBlock' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
      delete block;
             ^
chromDrawCPP/karyotype.cpp:315:13: warning: deleting object of polymorphic class type 'chCentromere' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
      delete centromere;
             ^
chromDrawCPP/karyotype.cpp:421:14: warning: deleting object of polymorphic class type 'markSign' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
       delete mark;
              ^
chromDrawCPP/karyotype.cpp:429:13: warning: deleting object of polymorphic class type 'markSign' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
      delete mark;
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDrawCPP/parameters.cpp -o chromDrawCPP/parameters.o
chromDrawCPP/parameters.cpp:66:21: warning: extra tokens at end of #ifdef directive
       #ifdef _WIN32 || _WIN64
                     ^
chromDrawCPP/parameters.cpp:147:15: warning: extra tokens at end of #ifdef directive
 #ifdef _WIN32 || _WIN64
               ^
chromDrawCPP/parameters.cpp:159:15: warning: extra tokens at end of #ifdef directive
 #ifdef _WIN32 || _WIN64
               ^
chromDrawCPP/parameters.cpp: In member function 'int parameters::loadArguments(int, char**)':
chromDrawCPP/parameters.cpp:47:19: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
         "--format"};
                   ^
chromDrawCPP/parameters.cpp:47:19: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
chromDrawCPP/parameters.cpp:47:19: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
chromDrawCPP/parameters.cpp:47:19: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
chromDrawCPP/parameters.cpp:47:19: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
chromDrawCPP/parameters.cpp:47:19: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
C:/Rtools/mingw_64/bin/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
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_init_chromDraw.cpp -o R_init_chromDraw.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chromDraw.cpp -o chromDraw.o
C:/Rtools/mingw_64/bin/ar crs libSn3.a R_init_chromDraw.o RcppExports.o chromDraw.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o chromDraw.dll tmp.def chromDraw.o RcppExports.o libSn1.a libSn2.a libSn3.a -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/chromDraw.buildbin-libdir/chromDraw/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chromDraw' as chromDraw_2.14.0.zip
* DONE (chromDraw)