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CHECK report for R4RNA on celaya2

This page was generated on 2020-01-16 13:43:47 -0500 (Thu, 16 Jan 2020).

Package 1358/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
R4RNA 1.15.0
Daniel Lai
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/R4RNA
Branch: master
Last Commit: 652639e
Last Changed Date: 2019-10-29 13:40:10 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: R4RNA
Version: 1.15.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:R4RNA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings R4RNA_1.15.0.tar.gz
StartedAt: 2020-01-16 07:55:30 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 07:57:45 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 135.5 seconds
RetCode: 0
Status:  OK 
CheckDir: R4RNA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:R4RNA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings R4RNA_1.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/R4RNA.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘R4RNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘R4RNA’ version ‘1.15.0’
* 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 ‘R4RNA’ 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
* 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 ... NOTE
alignmentCanonical: no visible global function definition for ‘is’
alignmentConservation: no visible global function definition for ‘is’
alignmentCovariation: no visible global function definition for ‘is’
alignmentPercentGaps: no visible global function definition for ‘is’
arc: no visible global function definition for ‘lines’
baseConservation: no visible global function definition for ‘is’
basepairCanonical: no visible global function definition for ‘is’
basepairConservation: no visible global function definition for ‘is’
basepairCovariation: no visible global function definition for ‘is’
blankPlot: no visible global function definition for ‘par’
blankPlot: no visible global function definition for ‘plot’
blankPlot: no visible global function definition for ‘abline’
colourByCanonical: no visible global function definition for ‘is’
colourByConservation: no visible global function definition for ‘is’
colourByCovariation: no visible global function definition for ‘is’
getBaseColours: no visible global function definition for ‘is’
getCovarianceColours: no visible global function definition for ‘is’
getSequenceColour: no visible global function definition for ‘is’
helixCanonical: no visible global function definition for ‘is’
helixConservation: no visible global function definition for ‘is’
helixCovariation: no visible global function definition for ‘is’
isConflictingHelix: no visible global function definition for
  ‘aggregate’
isDuplicatingHelix: no visible global function definition for
  ‘aggregate’
isOverlappingHelix: no visible global function definition for
  ‘aggregate’
plotArc: no visible global function definition for ‘lines’
plotArrow: no visible global function definition for ‘polygon’
plotCovariance: no visible global function definition for ‘is’
plotCovarianceGrid: no visible global function definition for ‘rect’
plotCovarianceLine: no visible global function definition for
  ‘segments’
plotDoubleCovariance: no visible global function definition for ‘is’
plotDoubleHelix: no visible global function definition for ‘lines’
plotHelix: no visible global function definition for ‘lines’
plotOverlapCovariance: no visible global function definition for ‘is’
plotOverlapHelix: no visible global function definition for ‘lines’
plotScale: no visible global function definition for ‘strheight’
plotScale: no visible global function definition for ‘segments’
plotScale: no visible global function definition for ‘text’
readConnect: no visible global function definition for ‘read.delim’
readHelix: no visible global function definition for ‘read.delim’
structureMismatchScore: no visible global function definition for ‘is’
writeHelix: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline aggregate is lines par plot polygon read.delim rect segments
  strheight text write.table
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot", "polygon",
             "rect", "segments", "strheight", "text")
  importFrom("methods", "is")
  importFrom("stats", "aggregate")
  importFrom("utils", "read.delim", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/R4RNA.Rcheck/00check.log’
for details.



Installation output

R4RNA.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL R4RNA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘R4RNA’ ...
** 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 (R4RNA)

Tests output


Example timings

R4RNA.Rcheck/R4RNA-Ex.timings

nameusersystemelapsed
R4RNA-package2.6520.1963.029
alignmentStatistics1.0550.0201.170
as.helix0.0040.0010.004
basepairFrequency0.0160.0080.024
blankPlot0.0710.0030.082
colourHelices0.5440.0190.585
expandCollapseHelix0.0170.0020.019
logicalHelix0.8800.0241.018
logseq0.0010.0010.001
plotCovariance1.0430.0221.110
plotHelix1.0200.0401.192
readStructure0.0630.0040.070
structureMismatchScore0.0070.0030.010
unknottedGroups0.0380.0050.043
viennaToHelix0.0880.0040.100
writeHelix0.0040.0010.005