Jan Janecka
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/chromDraw |
| Branch: master |
| Last Commit: 7b7ae11 |
| Last Changed Date: 2018-10-30 11:54:33 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:40:52 -0400 (Tue, 09 Apr 2019).
| Package 265/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| chromDraw 2.13.0 Jan Janecka
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: chromDraw |
| Version: 2.13.0 |
| 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_2.13.0.tar.gz |
| StartedAt: 2019-04-08 23:26:36 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:27:54 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 78.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: chromDraw.Rcheck |
| Warnings: 3 |
############################################################################## ############################################################################## ### ### 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_2.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/chromDraw.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * 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 ‘2.13.0’ * 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.
chromDraw.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL chromDraw
###
##############################################################################
##############################################################################
* 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)
chromDraw.Rcheck/chromDraw-Ex.timings
| name | user | system | elapsed | |
| chromDraw-package | 0.135 | 0.008 | 0.150 | |
| chromDraw | 0.143 | 0.004 | 0.148 | |
| chromDrawGR | 0.844 | 0.048 | 0.892 | |
| convertInputColors | 0.001 | 0.001 | 0.002 | |
| convertInputData | 0.700 | 0.002 | 0.702 | |
| main_chromDraw | 0.141 | 0.004 | 0.145 | |