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This page was generated on 2022-01-27 11:10:19 -0500 (Thu, 27 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
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 merida1


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 307/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromDraw 2.25.0  (landing page)
Jan Janecka
Snapshot Date: 2022-01-26 13:55:18 -0500 (Wed, 26 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    NA  
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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:chromDraw.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings chromDraw_2.25.0.tar.gz
StartedAt: 2022-01-26 23:17:05 -0500 (Wed, 26 Jan 2022)
EndedAt: 2022-01-26 23:19:01 -0500 (Wed, 26 Jan 2022)
EllapsedTime: 115.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: chromDraw.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:chromDraw.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings chromDraw_2.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/chromDraw.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘chromDraw’ can be installed ... WARNING
Found the following significant warnings:
  chromDrawCPP/parameters.cpp:42:30: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  chromDrawCPP/parameters.cpp:43:9: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  chromDrawCPP/parameters.cpp:44:9: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  chromDrawCPP/parameters.cpp:45:9: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  chromDrawCPP/parameters.cpp:46:9: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  chromDrawCPP/parameters.cpp:47:9: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
See ‘/Users/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 is not available
File ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/chromDraw/libs/chromDraw.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (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 sizes of PDF files under ‘inst/doc’ ... OK
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/chromDraw.Rcheck/00check.log’
for details.



Installation output

chromDraw.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL chromDraw
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘chromDraw’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c chromDraw.cpp -o chromDraw.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c libBoard/src/Board.cpp -o libBoard/src/Board.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c libBoard/src/Color.cpp -o libBoard/src/Color.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c libBoard/src/Path.cpp -o libBoard/src/Path.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c libBoard/src/Shapes.cpp -o libBoard/src/Shapes.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -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++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -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++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -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++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -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-abstract-non-virtual-dtor]
                                                delete block;
                                                ^
chromDrawCPP/karyotype.cpp:274:6: warning: delete called on non-final 'chBlock' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
                                        delete block;
                                        ^
chromDrawCPP/karyotype.cpp:315:6: warning: delete called on non-final 'chCentromere' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
                                        delete centromere;
                                        ^
chromDrawCPP/karyotype.cpp:421:7: warning: delete called on non-final 'markSign' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
                                                delete mark;
                                                ^
chromDrawCPP/karyotype.cpp:429:6: warning: delete called on non-final 'markSign' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
                                        delete mark;
                                        ^
5 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -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++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_chromDraw.cpp -o R_init_chromDraw.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 /Library/Frameworks/R.framework/Versions/4.2/Resources/library/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)

Tests output


Example timings

chromDraw.Rcheck/chromDraw-Ex.timings

nameusersystemelapsed
chromDraw-package0.0950.0150.111
chromDraw0.0830.0130.097
chromDrawGR1.5120.0451.562
convertInputColors0.0020.0010.002
convertInputData1.2000.0101.211
main_chromDraw0.0940.0130.107