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This page was generated on 2021-10-15 15:05:37 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the chromDraw package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chromDraw.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 303/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
chromDraw 2.22.0 (landing page) Jan Janecka
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: chromDraw |
Version: 2.22.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:chromDraw.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings chromDraw_2.22.0.tar.gz |
StartedAt: 2021-10-14 09:14:43 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:15:49 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 66.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: chromDraw.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:chromDraw.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings chromDraw_2.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/chromDraw.Rcheck’ * using R version 4.1.1 (2021-08-10) * 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 ‘2.22.0’ * 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:42:30: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] chromDrawCPP/parameters.cpp:43:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] chromDrawCPP/parameters.cpp:44:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] chromDrawCPP/parameters.cpp:45:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] chromDrawCPP/parameters.cpp:46:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] chromDrawCPP/parameters.cpp:47:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] See ‘/home/biocbuild/bbs-3.13-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 use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/home/biocbuild/bbs-3.13-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-3.13-bioc/meat/chromDraw.Rcheck/00check.log’ for details.
chromDraw.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL chromDraw ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘chromDraw’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDraw.cpp -o chromDraw.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-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++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-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++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-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++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-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++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-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++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-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++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-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++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-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++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-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++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-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] 266 | 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] 274 | 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] 315 | 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] 421 | 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] 429 | delete mark; | ^~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-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] 320 | 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] 396 | float coordinate_y; | ^~~~~~~~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-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] 47 | char x = argv[argcurent][1]; | ^ chromDrawCPP/getOpts.cpp:48:8: warning: unused variable ‘y’ [-Wunused-variable] 48 | char y = argv[argcurent][2]; | ^ chromDrawCPP/getOpts.cpp:49:8: warning: unused variable ‘o’ [-Wunused-variable] 49 | char o = optv[optcurent]; | ^ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-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::string, std::string)’: chromDrawCPP/ideogram.cpp:70:6: warning: ‘retVal’ may be used uninitialized in this function [-Wmaybe-uninitialized] 70 | int retVal; | ^~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-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 66 | #ifdef _WIN32 || _WIN64 | ^~ chromDrawCPP/parameters.cpp:147:15: warning: extra tokens at end of #ifdef directive 147 | #ifdef _WIN32 || _WIN64 | ^~ chromDrawCPP/parameters.cpp:159:15: warning: extra tokens at end of #ifdef directive 159 | #ifdef _WIN32 || _WIN64 | ^~ chromDrawCPP/parameters.cpp: In member function ‘int parameters::loadArguments(int, char**)’: chromDrawCPP/parameters.cpp:42:30: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 42 | char *paramsExpanded[10] = {"--help", | ^~~~~~~~ chromDrawCPP/parameters.cpp:43:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 43 | "--outputpath", | ^~~~~~~~~~~~~~ chromDrawCPP/parameters.cpp:44:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 44 | "--colorinputpath", | ^~~~~~~~~~~~~~~~~~ chromDrawCPP/parameters.cpp:45:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 45 | "--datainputpath", | ^~~~~~~~~~~~~~~~~ chromDrawCPP/parameters.cpp:46:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 46 | "--scale", | ^~~~~~~~~ chromDrawCPP/parameters.cpp:47:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 47 | "--format"}; | ^~~~~~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I'/home/biocbuild/bbs-3.13-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++14 -shared -L/home/biocbuild/bbs-3.13-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-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-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 | 0.095 | 0.008 | 0.105 | |
chromDraw | 0.086 | 0.012 | 0.098 | |
chromDrawGR | 1.064 | 0.071 | 1.136 | |
convertInputColors | 0.001 | 0.000 | 0.002 | |
convertInputData | 0.922 | 0.007 | 0.931 | |
main_chromDraw | 0.094 | 0.004 | 0.099 | |