chromDraw 2.6.0
Jan Janecka
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/chromDraw | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chromDraw_2.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/chromDraw.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.6.0’
* 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 ... 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. 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 ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
Object: ‘./libBoard/src/Tools.o’
Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
Objects: ‘chromDraw.o’, ‘./chromDrawCPP/colorPalette.o’,
‘./chromDrawCPP/ideogram.o’, ‘./chromDrawCPP/karyotype.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: 2 WARNINGs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/chromDraw.Rcheck/00check.log’
for details.
* installing *source* package ‘chromDraw’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c chromDraw.cpp -o chromDraw.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c libBoard/src/Board.cpp -o libBoard/src/Board.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c libBoard/src/Color.cpp -o libBoard/src/Color.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c libBoard/src/Path.cpp -o libBoard/src/Path.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c libBoard/src/Shapes.cpp -o libBoard/src/Shapes.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/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++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/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++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/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++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/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-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-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-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-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-virtual-dtor]
delete mark;
^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/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: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
char *paramsExpanded[10] = {"--help",
^
chromDrawCPP/parameters.cpp:43:9: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
"--outputpath",
^
chromDrawCPP/parameters.cpp:44:9: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
"--colorinputpath",
^
chromDrawCPP/parameters.cpp:45:9: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
"--datainputpath",
^
chromDrawCPP/parameters.cpp:46:9: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
"--scale",
^
chromDrawCPP/parameters.cpp:47:9: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-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++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_chromDraw.cpp -o R_init_chromDraw.o
clang++ -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 /Users/biocbuild/bbs-3.5-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)