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CHECK report for chromDraw on malbec2

This page was generated on 2019-10-16 12:05:57 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:chromDraw.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings chromDraw_2.14.0.tar.gz
StartedAt: 2019-10-16 00:31:18 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:32:36 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 77.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: chromDraw.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:chromDraw.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings chromDraw_2.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/chromDraw.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘2.14.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘chromDraw’ can be installed ... WARNING
Found the following significant warnings:
  chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/biocbuild/bbs-3.9-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 compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.9-bioc/R/library/chromDraw/libs/chromDraw.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘_ZSt4cout’, 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 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/chromDraw.Rcheck/00check.log’
for details.



Installation output

chromDraw.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL chromDraw
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘chromDraw’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c chromDraw.cpp -o chromDraw.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c libBoard/src/Color.cpp -o libBoard/src/Color.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c libBoard/src/Path.cpp -o libBoard/src/Path.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c libBoard/src/Board.cpp -o libBoard/src/Board.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c libBoard/src/Shapes.cpp -o libBoard/src/Shapes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -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;
             ^~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -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;
        ^~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -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];
        ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -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:70:6: warning: ‘retVal’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  int retVal;
      ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -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]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c R_init_chromDraw.cpp -o R_init_chromDraw.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o chromDraw.so chromDraw.o RcppExports.o ./libBoard/src/PSFonts.o ./libBoard/src/Color.o ./libBoard/src/Path.o ./libBoard/src/ShapeList.o ./libBoard/src/Rect.o ./libBoard/src/Transforms.o ./libBoard/src/Board.o ./libBoard/src/Tools.o ./libBoard/src/Shapes.o ./chromDrawCPP/chCentromere.o ./chromDrawCPP/karyotype.o ./chromDrawCPP/color.o ./chromDrawCPP/canvas.o ./chromDrawCPP/chromosome.o ./chromDrawCPP/markSign.o ./chromDrawCPP/getOpts.o ./chromDrawCPP/chBlock.o ./chromDrawCPP/ideogram.o ./chromDrawCPP/chromosomeSign.o ./chromDrawCPP/colorPalette.o ./chromDrawCPP/parameters.o ./chromDrawCPP/chromosomeElement.o ./chromDrawCPP/chromosomeMark.o ./R_init_chromDraw.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/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-package0.1530.0040.232
chromDraw0.1490.0080.156
chromDrawGR0.9690.0481.019
convertInputColors0.0010.0010.002
convertInputData0.6570.0020.659
main_chromDraw0.1040.0000.104