Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.1: CHECK report for chromDraw on morelia

This page was generated on 2015-10-09 09:42:33 -0700 (Fri, 09 Oct 2015).

Package 166/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromDraw 1.0.0
Jan Janecka
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/chromDraw
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: chromDraw
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chromDraw_1.0.0.tar.gz
StartedAt: 2015-10-09 00:15:32 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 00:17:31 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 119.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: chromDraw.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chromDraw_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/chromDraw.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.0.0’
* 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 ... [33s/37s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
  src/chromDrawCPP/Makefile
  src/libBoard/src/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘chromDraw/libs/chromDraw.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Object: ‘./libBoard/src/Tools.o’
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘chromDraw.o’, ‘./chromDrawCPP/colorPalette.o’,
      ‘./chromDrawCPP/ideogram.o’, ‘./chromDrawCPP/karyotype.o’,
      ‘./chromDrawCPP/parameters.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/7s] 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/chromDraw.Rcheck/00check.log’
for details.


chromDraw.Rcheck/00install.out:

* installing *source* package ‘chromDraw’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chromDraw.cpp -o chromDraw.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chromDrawCPP/canvas.cpp -o chromDrawCPP/canvas.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chromDrawCPP/chdrawer.cpp -o chromDrawCPP/chdrawer.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chromDrawCPP/getOpts.cpp -o chromDrawCPP/getOpts.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chromDrawCPP/ideogram.cpp -o chromDrawCPP/ideogram.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chromDrawCPP/karyotype.cpp -o chromDrawCPP/karyotype.o
chromDrawCPP/karyotype.cpp:265:7: warning: delete called on 'chBlock' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
                                                delete block;
                                                ^
chromDrawCPP/karyotype.cpp:273:6: warning: delete called on 'chBlock' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
                                        delete block;
                                        ^
chromDrawCPP/karyotype.cpp:312:6: warning: delete called on 'chCentromere' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
                                        delete centromere;
                                        ^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chromDrawCPP/parameters.cpp -o chromDrawCPP/parameters.o
chromDrawCPP/parameters.cpp:58:21: warning: extra tokens at end of #ifdef directive [-Wextra-tokens]
                                                #ifdef _WIN32 || _WIN64
                                                              ^
                                                              //
chromDrawCPP/parameters.cpp:123:15: warning: extra tokens at end of #ifdef directive [-Wextra-tokens]
#ifdef _WIN32 || _WIN64
              ^
              //
chromDrawCPP/parameters.cpp:135:15: warning: extra tokens at end of #ifdef directive [-Wextra-tokens]
#ifdef _WIN32 || _WIN64
              ^
              //
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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/chdrawer.o ./chromDrawCPP/chromosome.o ./chromDrawCPP/chromosomeElement.o ./chromDrawCPP/color.o ./chromDrawCPP/colorPalette.o ./chromDrawCPP/getOpts.o ./chromDrawCPP/ideogram.o ./chromDrawCPP/karyotype.o ./chromDrawCPP/parameters.o ./R_init_chromDraw.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/chromDraw.Rcheck/chromDraw/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (chromDraw)

chromDraw.Rcheck/chromDraw-Ex.timings:

nameusersystemelapsed
chromDraw-package0.0610.0160.165
chromDraw0.0640.0250.193
chromDrawGR1.4530.1921.991
convertInputColors0.0020.0000.002
convertInputData1.2870.0121.299
main_chromDraw0.0820.0190.100