Jan Janecka
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/chromDraw |
| Branch: RELEASE_3_7 |
| Last Commit: 75b3c75 |
| Last Changed Date: 2018-04-30 10:35:35 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:54:06 -0400 (Wed, 17 Oct 2018).
| Package 241/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| chromDraw 2.10.0 Jan Janecka
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: chromDraw |
| Version: 2.10.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:chromDraw.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings chromDraw_2.10.0.tar.gz |
| StartedAt: 2018-10-16 20:27:27 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 20:28:49 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 82.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: chromDraw.Rcheck |
| Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:chromDraw.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings chromDraw_2.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/chromDraw.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * 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 ‘2.10.0’ * 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 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 Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/3.5/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: 2 WARNINGs, 2 NOTEs See ‘/Users/biocbuild/bbs-3.7-bioc/meat/chromDraw.Rcheck/00check.log’ for details.
chromDraw.Rcheck/00install.out
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##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL chromDraw
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* 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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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 /Library/Frameworks/R.framework/Versions/3.5/Resources/library/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
* DONE (chromDraw)
chromDraw.Rcheck/chromDraw-Ex.timings
| name | user | system | elapsed | |
| chromDraw-package | 0.090 | 0.015 | 0.125 | |
| chromDraw | 0.068 | 0.009 | 0.077 | |
| chromDrawGR | 1.102 | 0.070 | 1.182 | |
| convertInputColors | 0.004 | 0.000 | 0.004 | |
| convertInputData | 0.848 | 0.005 | 0.855 | |
| main_chromDraw | 0.066 | 0.007 | 0.074 | |