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CHECK report for garfield on tokay1

This page was generated on 2018-04-12 13:27:33 -0400 (Thu, 12 Apr 2018).

Package 517/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
garfield 1.6.0
Valentina Iotchkova
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/garfield
Branch: RELEASE_3_6
Last Commit: c59253f
Last Changed Date: 2017-10-30 12:41:13 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: garfield
Version: 1.6.0
Command: rm -rf garfield.buildbin-libdir garfield.Rcheck && mkdir garfield.buildbin-libdir garfield.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=garfield.buildbin-libdir garfield_1.6.0.tar.gz >garfield.Rcheck\00install.out 2>&1 && cp garfield.Rcheck\00install.out garfield-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=garfield.buildbin-libdir --install="check:garfield-install.out" --force-multiarch --no-vignettes --timings garfield_1.6.0.tar.gz
StartedAt: 2018-04-12 00:07:38 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:08:59 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 80.6 seconds
RetCode: 0
Status:  OK  
CheckDir: garfield.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf garfield.buildbin-libdir garfield.Rcheck && mkdir garfield.buildbin-libdir garfield.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=garfield.buildbin-libdir garfield_1.6.0.tar.gz >garfield.Rcheck\00install.out 2>&1 && cp garfield.Rcheck\00install.out garfield-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=garfield.buildbin-libdir --install="check:garfield-install.out" --force-multiarch --no-vignettes --timings garfield_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/garfield.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'garfield/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'garfield' version '1.6.0'
* 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 'garfield' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
** checking loading without being on the library search path ... 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 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 ... NOTE
garfield.plot: no visible global function definition for 'read.table'
garfield.plot: no visible global function definition for
  'colorRampPalette'
garfield.plot: no visible global function definition for 'pdf'
garfield.plot: no visible global function definition for 'layout'
garfield.plot: no visible global function definition for 'par'
garfield.plot: no visible global function definition for 'title'
garfield.plot: no visible global function definition for 'plot'
garfield.plot: no visible global function definition for 'legend'
garfield.plot: no visible global function definition for 'dev.off'
garfield.plot.fnx: no visible global function definition for 'par'
garfield.plot.fnx: no visible global function definition for 'plot'
garfield.plot.fnx: no visible global function definition for 'polygon'
garfield.plot.fnx: no visible global function definition for 'segments'
garfield.plot.fnx: no visible global function definition for 'points'
garfield.plot.fnx: no visible global function definition for 'lines'
garfield.plot.fnx: no visible global function definition for 'median'
garfield.plot.fnx: no visible global function definition for 'text'
Undefined global functions or variables:
  colorRampPalette dev.off layout legend lines median par pdf plot
  points polygon read.table segments text title
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
  importFrom("graphics", "layout", "legend", "lines", "par", "plot",
             "points", "polygon", "segments", "text", "title")
  importFrom("stats", "median")
  importFrom("utils", "read.table")
to your NAMESPACE file.
* 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 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-3.6-bioc/meat/garfield.buildbin-libdir/garfield/libs/i386/garfield.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
garfield.plot 7.64   0.09    7.74
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
garfield.plot 7.15   0.14     7.3
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/garfield.Rcheck/00check.log'
for details.



Installation output

garfield.Rcheck/00install.out


install for i386

* installing *source* package 'garfield' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c garfield_init.c -o garfield_init.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c garfield_perm.cpp -o garfield_perm.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c garfield_prep.cpp -o garfield_prep.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o garfield.dll tmp.def garfield_init.o garfield_perm.o garfield_prep.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/garfield.buildbin-libdir/garfield/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'garfield'
    finding HTML links ... done
    garfield-package                        html  
    garfield.plot                           html  
    garfield.plot.fnx                       html  
    garfield.run                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'garfield' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c garfield_init.c -o garfield_init.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c garfield_perm.cpp -o garfield_perm.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c garfield_prep.cpp -o garfield_prep.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o garfield.dll tmp.def garfield_init.o garfield_perm.o garfield_prep.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/garfield.buildbin-libdir/garfield/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'garfield' as garfield_1.6.0.zip
* DONE (garfield)
In R CMD INSTALL
In R CMD INSTALL

Tests output


Example timings

garfield.Rcheck/examples_i386/garfield-Ex.timings

nameusersystemelapsed
garfield.plot7.640.097.74
garfield.plot.fnx000
garfield.run0.830.140.97

garfield.Rcheck/examples_x64/garfield-Ex.timings

nameusersystemelapsed
garfield.plot7.150.147.30
garfield.plot.fnx0.020.000.01
garfield.run0.810.060.88