Multiple platform build/check report for BioC 3.21 - INSTALL results for chromDraw on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4754
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4472
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4426
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4381
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4373
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*
INSTALL results for chromDraw on palomino7

To the developers/maintainers of the chromDraw package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chromDraw.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
raw results
Summary

Package: chromDraw
Version: 2.37.0
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL chromDraw
StartedAt: 2024-12-23 15:33:17 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 15:33:58 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 41.1 seconds
RetCode: 1
Status: ERROR
Command output

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###
### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL chromDraw
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'chromDraw' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c libBoard/src/Board.cpp -o libBoard/src/Board.o
In file included from ./libBoard/include/board/Tools.h:102,
                 from ./libBoard/include/board/Shapes.h:51,
                 from ./libBoard/include/Board.h:51,
                 from libBoard/src/Board.cpp:43:
In function 'void LibBoard::secured_ctime(char*, const time_t*, size_t)',
    inlined from 'void LibBoard::Board::saveEPS(const char*, double, double, double) const' at libBoard/src/Board.cpp:760:18:
./libBoard/include/board/Tools.ih:27:10: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 255 equals destination size [-Wstringop-truncation]
   27 |   strncpy( str, ctime(t), count );
      |   ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c libBoard/src/Color.cpp -o libBoard/src/Color.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c libBoard/src/Path.cpp -o libBoard/src/Path.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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*)&<unnamed> + 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: '<anonymous>' 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: '<unnamed>.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: '<anonymous>' 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: '<unnamed>.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: '<anonymous>' declared here
  238 |   return Point(*this).rotate( angle, center );
      |                     ^
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o
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
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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"};
      |                                                                 ^~~~~~~~~~
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
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c R_init_chromDraw.cpp -o R_init_chromDraw.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c chromDraw.cpp -o chromDraw.o
ar crs libSn3.a R_init_chromDraw.o RcppExports.o chromDraw.o
g++ -std=gnu++17 -shared -s -static-libgcc -o chromDraw.dll tmp.def chromDraw.o RcppExports.o libSn1.a libSn2.a libSn3.a -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(markSign.o):markSign.cpp:(.rdata$.refptr._ZN8LibBoard5Color5BlackE[.refptr._ZN8LibBoard5Color5BlackE]+0x0): undefined reference to `LibBoard::Color::Black'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x166): undefined reference to `LibBoard::Board::setPenColorRGBi(unsigned char, unsigned char, unsigned char, unsigned char)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x176): undefined reference to `LibBoard::Board::setLineWidth(double)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x1ed): undefined reference to `LibBoard::Board::setPenColorRGBi(unsigned char, unsigned char, unsigned char, unsigned char)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x20d): undefined reference to `LibBoard::Board::drawDot(double, double, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x232): undefined reference to `LibBoard::Board::drawDot(double, double, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x2c9): undefined reference to `LibBoard::Board::saveSVG(char const*, LibBoard::Board::PageSize, double) const'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x36b): undefined reference to `LibBoard::Board::saveEPS(char const*, LibBoard::Board::PageSize, double) const'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x40c): undefined reference to `LibBoard::Board::setFillColorRGBi(unsigned char, unsigned char, unsigned char, unsigned char)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x467): undefined reference to `LibBoard::Board::setFillColorRGBi(unsigned char, unsigned char, unsigned char, unsigned char)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x565): undefined reference to `LibBoard::Board::setLineWidth(double)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x574): undefined reference to `LibBoard::Board::setPenColor(LibBoard::Color const&)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x5bc): undefined reference to `LibBoard::Board::drawRectangle(double, double, double, double, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x633): undefined reference to `LibBoard::Board::setLineWidth(double)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x642): undefined reference to `LibBoard::Board::setPenColor(LibBoard::Color const&)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x691): undefined reference to `LibBoard::Board::drawLine(double, double, double, double, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x6d0): undefined reference to `LibBoard::Board::drawLine(double, double, double, double, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x704): undefined reference to `LibBoard::Board::drawLine(double, double, double, double, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x73c): undefined reference to `LibBoard::Board::drawLine(double, double, double, double, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x7b5): undefined reference to `LibBoard::Board::setPenColor(LibBoard::Color const&)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x7ce): undefined reference to `LibBoard::Board::setFont(LibBoard::Fonts::Font, double)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x8a4): undefined reference to `LibBoard::Board::drawText(double, double, char const*, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x998): undefined reference to `LibBoard::Board::setPenColor(LibBoard::Color const&)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x9b1): undefined reference to `LibBoard::Board::setFont(LibBoard::Fonts::Font, double)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0xa9e): undefined reference to `LibBoard::Board::drawText(double, double, char const*, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0xb36): undefined reference to `LibBoard::Board::setLineWidth(double)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0xb4a): undefined reference to `LibBoard::Board::setPenColor(LibBoard::Color const&)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0xc2b): undefined reference to `LibBoard::Board::drawRectangle(double, double, double, double, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0xe16): undefined reference to `LibBoard::Board::setLineWidth(double)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0xe29): undefined reference to `LibBoard::Board::setPenColor(LibBoard::Color const&)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0xef6): undefined reference to `LibBoard::Board::drawEllipse(double, double, double, double, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x10fe): undefined reference to `LibBoard::Board::setPenColor(LibBoard::Color const&)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x1119): undefined reference to `LibBoard::Board::setFont(LibBoard::Fonts::Font, double)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x11a1): undefined reference to `LibBoard::Board::drawText(double, double, char const*, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x161a): undefined reference to `LibBoard::Board::setLineWidth(double)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x1629): undefined reference to `LibBoard::Board::setPenColor(LibBoard::Color const&)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x164f): undefined reference to `LibBoard::Board::drawLine(double, double, double, double, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x1674): undefined reference to `LibBoard::Board::drawLine(double, double, double, double, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x1699): undefined reference to `LibBoard::Board::drawLine(double, double, double, double, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x16bf): undefined reference to `LibBoard::Board::drawLine(double, double, double, double, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x18bf): undefined reference to `LibBoard::Board::setPenColor(LibBoard::Color const&)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x18d8): undefined reference to `LibBoard::Board::setFont(LibBoard::Fonts::Font, double)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x18f3): undefined reference to `LibBoard::Board::drawText(double, double, char const*, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x1b14): undefined reference to `LibBoard::Board::setPenColor(LibBoard::Color const&)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x1b2f): undefined reference to `LibBoard::Board::setFont(LibBoard::Fonts::Font, double)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x1b8d): undefined reference to `LibBoard::Board::drawText(double, double, char const*, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x1dc1): undefined reference to `LibBoard::Board::setPenColor(LibBoard::Color const&)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x1de0): undefined reference to `LibBoard::Board::setFont(LibBoard::Fonts::Font, double)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x1dfc): undefined reference to `LibBoard::Board::drawText(double, double, char const*, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x2173): undefined reference to `LibBoard::Board::setLineWidth(double)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x2182): undefined reference to `LibBoard::Board::setPenColor(LibBoard::Color const&)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x2257): undefined reference to `LibBoard::Board::drawRectangle(double, double, double, double, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x2402): undefined reference to `LibBoard::Board::setLineWidth(double)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x2411): undefined reference to `LibBoard::Board::setPenColor(LibBoard::Color const&)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x24db): undefined reference to `LibBoard::Board::drawEllipse(double, double, double, double, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x2958): undefined reference to `LibBoard::Board::setLineWidth(double)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x296a): undefined reference to `LibBoard::Board::setPenColor(LibBoard::Color const&)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x2975): undefined reference to `LibBoard::Board::setFillColor(LibBoard::Color const&)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x2988): undefined reference to `LibBoard::Board::drawClosedPolyline(std::vector<LibBoard::Point, std::allocator<LibBoard::Point> > const&, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x2bee): undefined reference to `LibBoard::Board::setLineWidth(double)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x2c00): undefined reference to `LibBoard::Board::setPenColor(LibBoard::Color const&)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x2c0b): undefined reference to `LibBoard::Board::setFillColor(LibBoard::Color const&)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x2c1c): undefined reference to `LibBoard::Board::drawClosedPolyline(std::vector<LibBoard::Point, std::allocator<LibBoard::Point> > const&, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x2f28): undefined reference to `LibBoard::Board::setLineWidth(double)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x2f37): undefined reference to `LibBoard::Board::setPenColor(LibBoard::Color const&)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x2f48): undefined reference to `LibBoard::Board::drawClosedPolyline(std::vector<LibBoard::Point, std::allocator<LibBoard::Point> > const&, int)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x2fed): undefined reference to `LibBoard::Board::Board(LibBoard::Color const&)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x300a): undefined reference to `LibBoard::Board::setPenColorRGBi(unsigned char, unsigned char, unsigned char, unsigned char)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x301a): undefined reference to `LibBoard::Board::setLineWidth(double)'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x3053): undefined reference to `LibBoard::Board::~Board()'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.text+0x307d): undefined reference to `LibBoard::Board::~Board()'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.rdata$.refptr._ZN8LibBoard5Color4NoneE[.refptr._ZN8LibBoard5Color4NoneE]+0x0): undefined reference to `LibBoard::Color::None'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.rdata$.refptr._ZN8LibBoard5Board6DegreeE[.refptr._ZN8LibBoard5Board6DegreeE]+0x0): undefined reference to `LibBoard::Board::Degree'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: libSn2.a(canvas.o):canvas.cpp:(.rdata$.refptr._ZN8LibBoard5errorE[.refptr._ZN8LibBoard5errorE]+0x0): undefined reference to `LibBoard::error'
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'chromDraw'
* removing 'E:/biocbuild/bbs-3.21-bioc/R/library/chromDraw'