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This page was generated on 2021-10-15 15:06:00 -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: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chromDraw.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings chromDraw_2.22.0.tar.gz |
StartedAt: 2021-10-14 21:00:42 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 21:02:48 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 125.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: chromDraw.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chromDraw.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings chromDraw_2.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/chromDraw.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * 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 whether package 'chromDraw' can be installed ... WARNING Found the following significant warnings: ./libBoard/include/board/Tools.ih:27:10: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 255 equals destination size [-Wstringop-truncation] chromDrawCPP/parameters.cpp:47:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] ./libBoard/include/board/Point.h:71:40: warning: '<anonymous>' is used uninitialized in this function [-Wuninitialized] ./libBoard/include/board/Point.h:71:51: warning: '*((void*)&<anonymous> +8)' is used uninitialized in this function [-Wuninitialized] See 'C:/Users/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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/chromDraw/libs/i386/chromDraw.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/chromDraw/libs/x64/chromDraw.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.13-bioc/meat/chromDraw.Rcheck/00check.log' for details.
chromDraw.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/chromDraw_2.22.0.tar.gz && rm -rf chromDraw.buildbin-libdir && mkdir chromDraw.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chromDraw.buildbin-libdir chromDraw_2.22.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL chromDraw_2.22.0.zip && rm chromDraw_2.22.0.tar.gz chromDraw_2.22.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 67 1225k 67 830k 0 0 1472k 0 --:--:-- --:--:-- --:--:-- 1472k 100 1225k 100 1225k 0 0 1717k 0 --:--:-- --:--:-- --:--:-- 1716k install for i386 * installing *source* package 'chromDraw' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Shapes.cpp -o libBoard/src/Shapes.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Board.cpp -o libBoard/src/Board.o In file included from ./libBoard/include/board/Tools.h:102, from ./libBoard/include/board/Shapes.h:51, from ./libBoard/include/Board.h:51, from libBoard/src/Board.cpp:43: In function 'void LibBoard::secured_ctime(char*, const time_t*, size_t)', inlined from 'void LibBoard::Board::saveEPS(const char*, double, double, double) const' at libBoard/src/Board.cpp:760:18: ./libBoard/include/board/Tools.ih:27:10: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 255 equals destination size [-Wstringop-truncation] strncpy( str, ctime(t), count ); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Path.cpp -o libBoard/src/Path.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Color.cpp -o libBoard/src/Color.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o "C:/rtools40/mingw32/bin/"ar crs libSn1.a libBoard/src/Shapes.o libBoard/src/Tools.o libBoard/src/Board.o libBoard/src/Transforms.o libBoard/src/Rect.o libBoard/src/ShapeList.o libBoard/src/Path.o libBoard/src/Color.o libBoard/src/PSFonts.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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] "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:80:2: warning: 'retVal' may be used uninitialized in this function [-Wmaybe-uninitialized] if(retVal != 0) ^~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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]; ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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; ^~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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; ^~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o "C:/rtools40/mingw32/bin/"ar crs libSn2.a chromDrawCPP/chromosomeMark.o chromDrawCPP/chromosomeElement.o chromDrawCPP/parameters.o chromDrawCPP/colorPalette.o chromDrawCPP/chromosomeSign.o chromDrawCPP/ideogram.o chromDrawCPP/chBlock.o chromDrawCPP/getOpts.o chromDrawCPP/markSign.o chromDrawCPP/chromosome.o chromDrawCPP/canvas.o chromDrawCPP/color.o chromDrawCPP/karyotype.o chromDrawCPP/chCentromere.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDraw.cpp -o chromDraw.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_chromDraw.cpp -o R_init_chromDraw.o "C:/rtools40/mingw32/bin/"ar crs libSn3.a RcppExports.o chromDraw.o R_init_chromDraw.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o chromDraw.dll tmp.def chromDraw.o RcppExports.o libSn1.a libSn2.a libSn3.a -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/chromDraw.buildbin-libdir/00LOCK-chromDraw/00new/chromDraw/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'chromDraw' finding HTML links ... done chromDraw-package html chromDraw html chromDrawGR html convertInputColors html convertInputData html main_chromDraw html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'chromDraw' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Shapes.cpp -o libBoard/src/Shapes.o In file included from ./libBoard/include/board/Rect.h:46, from libBoard/src/Shapes.cpp:42: ./libBoard/include/board/Point.h: In member function 'virtual LibBoard::Ellipse& LibBoard::Ellipse::rotate(double, const LibBoard::Point&)': ./libBoard/include/board/Point.h:71:40: warning: '<anonymous>' is used uninitialized in this function [-Wuninitialized] Point( const Point & other ):x(other.x),y(other.y) { } ~~~~~~^ ./libBoard/include/board/Point.h:71:51: warning: '*((void*)&<anonymous> +8)' is used uninitialized in this function [-Wuninitialized] Point( const Point & other ):x(other.x),y(other.y) { } ~~~~~~^ ./libBoard/include/board/Point.h:71:40: warning: '<anonymous>' is used uninitialized in this function [-Wuninitialized] Point( const Point & other ):x(other.x),y(other.y) { } ~~~~~~^ ./libBoard/include/board/Point.h:71:51: warning: '*((void*)&<anonymous> +8)' is used uninitialized in this function [-Wuninitialized] Point( const Point & other ):x(other.x),y(other.y) { } ~~~~~~^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Board.cpp -o libBoard/src/Board.o In file included from ./libBoard/include/board/Tools.h:102, from ./libBoard/include/board/Shapes.h:51, from ./libBoard/include/Board.h:51, from libBoard/src/Board.cpp:43: In function 'void LibBoard::secured_ctime(char*, const time_t*, size_t)', inlined from 'void LibBoard::Board::saveEPS(const char*, double, double, double) const' at libBoard/src/Board.cpp:760:18: ./libBoard/include/board/Tools.ih:27:10: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 255 equals destination size [-Wstringop-truncation] strncpy( str, ctime(t), count ); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Path.cpp -o libBoard/src/Path.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/Color.cpp -o libBoard/src/Color.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o "C:/rtools40/mingw64/bin/"ar crs libSn1.a libBoard/src/Shapes.o libBoard/src/Tools.o libBoard/src/Board.o libBoard/src/Transforms.o libBoard/src/Rect.o libBoard/src/ShapeList.o libBoard/src/Path.o libBoard/src/Color.o libBoard/src/PSFonts.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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] "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:80:2: warning: 'retVal' may be used uninitialized in this function [-Wmaybe-uninitialized] if(retVal != 0) ^~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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]; ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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; ^~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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; ^~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o "C:/rtools40/mingw64/bin/"ar crs libSn2.a chromDrawCPP/chromosomeMark.o chromDrawCPP/chromosomeElement.o chromDrawCPP/parameters.o chromDrawCPP/colorPalette.o chromDrawCPP/chromosomeSign.o chromDrawCPP/ideogram.o chromDrawCPP/chBlock.o chromDrawCPP/getOpts.o chromDrawCPP/markSign.o chromDrawCPP/chromosome.o chromDrawCPP/canvas.o chromDrawCPP/color.o chromDrawCPP/karyotype.o chromDrawCPP/chCentromere.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chromDraw.cpp -o chromDraw.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I./libBoard/include -I./chromDrawCPP -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_chromDraw.cpp -o R_init_chromDraw.o "C:/rtools40/mingw64/bin/"ar crs libSn3.a RcppExports.o chromDraw.o R_init_chromDraw.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o chromDraw.dll tmp.def chromDraw.o RcppExports.o libSn1.a libSn2.a libSn3.a -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/chromDraw.buildbin-libdir/chromDraw/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'chromDraw' as chromDraw_2.22.0.zip * DONE (chromDraw) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'chromDraw' successfully unpacked and MD5 sums checked
chromDraw.Rcheck/examples_i386/chromDraw-Ex.timings
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chromDraw.Rcheck/examples_x64/chromDraw-Ex.timings
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