chromDraw 2.3.0
Jan Janecka
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/chromDraw | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings chromDraw_2.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/chromDraw.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.3.0’
* 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 ... OK
* 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 loading without being on the library search path ... 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 ... OK
* 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. 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
File ‘chromDraw/libs/chromDraw.so’:
Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
Object: ‘./libBoard/src/Tools.o’
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Objects: ‘chromDraw.o’, ‘./chromDrawCPP/karyotype.o’,
‘./chromDrawCPP/ideogram.o’, ‘./chromDrawCPP/colorPalette.o’,
‘./chromDrawCPP/parameters.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘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: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/chromDraw.Rcheck/00check.log’
for details.
* installing *source* package ‘chromDraw’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c chromDraw.cpp -o chromDraw.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c libBoard/src/Color.cpp -o libBoard/src/Color.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c libBoard/src/Path.cpp -o libBoard/src/Path.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c libBoard/src/Board.cpp -o libBoard/src/Board.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c libBoard/src/Shapes.cpp -o libBoard/src/Shapes.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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 behaviour [-Wdelete-non-virtual-dtor]
delete block;
^
chromDrawCPP/karyotype.cpp:274:13: warning: deleting object of polymorphic class type ‘chBlock’ which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
delete block;
^
chromDrawCPP/karyotype.cpp:315:13: warning: deleting object of polymorphic class type ‘chCentromere’ which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
delete centromere;
^
chromDrawCPP/karyotype.cpp:421:14: warning: deleting object of polymorphic class type ‘markSign’ which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
delete mark;
^
chromDrawCPP/karyotype.cpp:429:13: warning: deleting object of polymorphic class type ‘markSign’ which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
delete mark;
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
"--format"};
^
chromDrawCPP/parameters.cpp:47:19: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
chromDrawCPP/parameters.cpp:47:19: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
chromDrawCPP/parameters.cpp:47:19: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
chromDrawCPP/parameters.cpp:47:19: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
chromDrawCPP/parameters.cpp:47:19: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c R_init_chromDraw.cpp -o R_init_chromDraw.o
g++ -shared -L/home/biocbuild/bbs-3.4-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-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/chromDraw.Rcheck/chromDraw/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (chromDraw)