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CHECK report for matchBox on merida1

This page was generated on 2020-04-15 12:38:14 -0400 (Wed, 15 Apr 2020).

Package 962/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
matchBox 1.28.0
Luigi Marchionni , Anuj Gupta
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/matchBox
Branch: RELEASE_3_10
Last Commit: 78691ef
Last Changed Date: 2019-10-29 13:08:35 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: matchBox
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:matchBox.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings matchBox_1.28.0.tar.gz
StartedAt: 2020-04-15 03:34:41 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 03:35:05 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 25.0 seconds
RetCode: 0
Status:  OK 
CheckDir: matchBox.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:matchBox.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings matchBox_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/matchBox.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘matchBox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘matchBox’ version ‘1.28.0’
* 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 ‘matchBox’ can be installed ... 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* 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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/matchBox.Rcheck/00check.log’
for details.



Installation output

matchBox.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL matchBox
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘matchBox’ ...
** using staged installation
** R
** data
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (matchBox)

Tests output


Example timings

matchBox.Rcheck/matchBox-Ex.timings

nameusersystemelapsed
calcHypPI0.1020.0070.112
computeCat0.2050.0290.236
filterRedundant0.0270.0060.033
mergeData0.0480.0020.050
plotCat0.1400.0130.154