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CHECK report for matchBox on tokay1

This page was generated on 2018-04-12 13:22:14 -0400 (Thu, 12 Apr 2018).

Package 791/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
matchBox 1.20.0
Luigi Marchionni , Anuj Gupta
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/matchBox
Branch: RELEASE_3_6
Last Commit: e74efea
Last Changed Date: 2017-10-30 12:39:54 -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 [ WARNINGS ] 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: matchBox
Version: 1.20.0
Command: rm -rf matchBox.buildbin-libdir matchBox.Rcheck && mkdir matchBox.buildbin-libdir matchBox.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=matchBox.buildbin-libdir matchBox_1.20.0.tar.gz >matchBox.Rcheck\00install.out 2>&1 && cp matchBox.Rcheck\00install.out matchBox-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=matchBox.buildbin-libdir --install="check:matchBox-install.out" --force-multiarch --no-vignettes --timings matchBox_1.20.0.tar.gz
StartedAt: 2018-04-12 01:09:24 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:09:50 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 26.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: matchBox.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf matchBox.buildbin-libdir matchBox.Rcheck && mkdir matchBox.buildbin-libdir matchBox.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=matchBox.buildbin-libdir matchBox_1.20.0.tar.gz >matchBox.Rcheck\00install.out 2>&1 && cp matchBox.Rcheck\00install.out matchBox-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=matchBox.buildbin-libdir --install="check:matchBox-install.out" --force-multiarch --no-vignettes --timings matchBox_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/matchBox.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 'matchBox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'matchBox' version '1.20.0'
* 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 'matchBox' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa82cs8/R.INSTALLdb07ff437de/matchBox/man/calcHypPI.Rd:96: missing file link 'qhyper'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa82cs8/R.INSTALLdb07ff437de/matchBox/man/plotCat.Rd:125: missing file link 'rainbow'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/matchBox.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
** 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'is.odd'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calcHypPI : <anonymous>: no visible global function definition for
  'qhyper'
computeCat: no visible global function definition for 'combn'
medianM: no visible global function definition for 'median'
plotCat: no visible global function definition for 'layout'
plotCat: no visible global function definition for 'rainbow'
plotCat: no visible global function definition for 'par'
plotCat: no visible global function definition for 'plot'
plotCat: no visible global function definition for 'colors'
plotCat: no visible global function definition for 'polygon'
plotCat: no visible global function definition for 'points'
plotCat: no visible global function definition for 'mtext'
plotCat: no visible global function definition for 'plot.new'
Undefined global functions or variables:
  colors combn layout median mtext par plot plot.new points polygon
  qhyper rainbow
Consider adding
  importFrom("grDevices", "colors", "rainbow")
  importFrom("graphics", "layout", "mtext", "par", "plot", "plot.new",
             "points", "polygon")
  importFrom("stats", "median", "qhyper")
  importFrom("utils", "combn")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* 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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/matchBox.Rcheck/00check.log'
for details.



Installation output

matchBox.Rcheck/00install.out


install for i386

* installing *source* package 'matchBox' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'matchBox'
    finding HTML links ... done
    calcHypPI                               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa82cs8/R.INSTALLdb07ff437de/matchBox/man/calcHypPI.Rd:96: missing file link 'qhyper'
    computeCat                              html  
    filterRedundant                         html  
    matchBox-package                        html  
    matchBoxExpression                      html  
    mergeData                               html  
    plotCat                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa82cs8/R.INSTALLdb07ff437de/matchBox/man/plotCat.Rd:125: missing file link 'rainbow'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'matchBox' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'matchBox' as matchBox_1.20.0.zip
* DONE (matchBox)
In R CMD INSTALL
In R CMD INSTALL

Tests output


Example timings

matchBox.Rcheck/examples_i386/matchBox-Ex.timings

nameusersystemelapsed
calcHypPI0.150.000.16
computeCat0.250.030.28
filterRedundant0.020.000.02
mergeData0.030.000.03
plotCat0.270.000.26

matchBox.Rcheck/examples_x64/matchBox-Ex.timings

nameusersystemelapsed
calcHypPI0.170.000.19
computeCat0.360.000.35
filterRedundant0.010.000.02
mergeData0.050.000.04
plotCat0.270.000.27