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This page was generated on 2022-01-21 11:07:12 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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

CHECK results for chromDraw on riesling1


To the developers/maintainers of the chromDraw package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 307/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromDraw 2.25.0  (landing page)
Jan Janecka
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/chromDraw
git_branch: master
git_last_commit: 8c2daf3
git_last_commit_date: 2021-10-26 12:18:12 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: chromDraw
Version: 2.25.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chromDraw.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings chromDraw_2.25.0.tar.gz
StartedAt: 2022-01-20 18:29:22 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 18:30:46 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 83.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: chromDraw.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chromDraw.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings chromDraw_2.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/chromDraw.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chromDraw/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chromDraw' version '2.25.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'chromDraw' can be installed ... WARNING
Found the following significant warnings:
  ./libBoard/include/board/Point.h:71:40: warning: '<anonymous>' is used uninitialized in this function [-Wuninitialized]
  ./libBoard/include/board/Point.h:71:51: warning: '*((void*)&<anonymous> +8)' is used uninitialized in this function [-Wuninitialized]
  ./libBoard/include/board/Tools.ih:27:10: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 255 equals destination size [-Wstringop-truncation]
  chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
See 'D:/biocbuild/bbs-3.15-bioc/meat/chromDraw.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... WARNING
Non-portable flags in variable 'PKG_CPPFLAGS':
  -isystem -isystem
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section 'Writing portable
packages' in the 'Writing R Extensions' manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/chromDraw/libs/x64/chromDraw.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 2 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/chromDraw.Rcheck/00check.log'
for details.



Installation output

chromDraw.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL chromDraw
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'chromDraw' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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:
./libBoard/include/board/Point.h: In member function 'virtual LibBoard::Ellipse& LibBoard::Ellipse::rotate(double, const LibBoard::Point&)':
./libBoard/include/board/Point.h:71:40: warning: '<anonymous>' is used uninitialized in this function [-Wuninitialized]
   Point( const Point & other ):x(other.x),y(other.y) { }
                                  ~~~~~~^
./libBoard/include/board/Point.h:71:51: warning: '*((void*)&<anonymous> +8)' is used uninitialized in this function [-Wuninitialized]
   Point( const Point & other ):x(other.x),y(other.y) { }
                                             ~~~~~~^
./libBoard/include/board/Point.h:71:40: warning: '<anonymous>' is used uninitialized in this function [-Wuninitialized]
   Point( const Point & other ):x(other.x),y(other.y) { }
                                  ~~~~~~^
./libBoard/include/board/Point.h:71:51: warning: '*((void*)&<anonymous> +8)' is used uninitialized in this function [-Wuninitialized]
   Point( const Point & other ):x(other.x),y(other.y) { }
                                             ~~~~~~^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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]
   strncpy( str, ctime(t), count );
   ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c libBoard/src/Path.cpp -o libBoard/src/Path.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c libBoard/src/Color.cpp -o libBoard/src/Color.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o
"C:/rtools40/mingw64/bin/"ar crs libSn1.a libBoard/src/Shapes.o libBoard/src/Tools.o libBoard/src/Board.o libBoard/src/Transforms.o libBoard/src/Rect.o libBoard/src/ShapeList.o libBoard/src/Path.o libBoard/src/Color.o libBoard/src/PSFonts.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
         "--format"};
                   ^
chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c chromDrawCPP/ideogram.cpp -o chromDrawCPP/ideogram.o
chromDrawCPP/ideogram.cpp: In member function 'int ideogram::loadMatrix(std::__cxx11::string, std::__cxx11::string)':
chromDrawCPP/ideogram.cpp:80:2: warning: 'retVal' may be used uninitialized in this function [-Wmaybe-uninitialized]
  if(retVal != 0)
  ^~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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 behavior [-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 behavior [-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 behavior [-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 behavior [-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 behavior [-Wdelete-non-virtual-dtor]
      delete mark;
             ^~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o
"C:/rtools40/mingw64/bin/"ar crs libSn2.a chromDrawCPP/chromosomeMark.o chromDrawCPP/chromosomeElement.o chromDrawCPP/parameters.o chromDrawCPP/colorPalette.o chromDrawCPP/chromosomeSign.o chromDrawCPP/ideogram.o chromDrawCPP/chBlock.o chromDrawCPP/getOpts.o chromDrawCPP/markSign.o chromDrawCPP/chromosome.o chromDrawCPP/canvas.o chromDrawCPP/color.o chromDrawCPP/karyotype.o chromDrawCPP/chCentromere.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c chromDraw.cpp -o chromDraw.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c R_init_chromDraw.cpp -o R_init_chromDraw.o
"C:/rtools40/mingw64/bin/"ar crs libSn3.a RcppExports.o chromDraw.o R_init_chromDraw.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -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 -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-chromDraw/00new/chromDraw/libs/x64
** 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
* DONE (chromDraw)
Making 'packages.html' ... done

Tests output


Example timings

chromDraw.Rcheck/chromDraw-Ex.timings

nameusersystemelapsed
chromDraw-package0.150.000.16
chromDraw0.140.000.14
chromDrawGR0.670.080.77
convertInputColors000
convertInputData0.440.000.44
main_chromDraw0.150.031.33