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CHECK report for R4RNA on machv2

This page was generated on 2020-10-17 11:59:20 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE R4RNA PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1409/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
R4RNA 1.16.0
Daniel Lai
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/R4RNA
Branch: RELEASE_3_11
Last Commit: ccaa37f
Last Changed Date: 2020-04-27 14:52:36 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: R4RNA
Version: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2020-10-17 04:20:12 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:22:00 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 107.4 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_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/R4RNA.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.16.0’
* 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 ‘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 polygon read.delim rect segments
  strheight text write.table
Consider adding
  importFrom("graphics", "abline", "lines", "par", "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-package2.1150.1122.234
alignmentStatistics0.7960.0280.856
as.helix0.0040.0010.004
basepairFrequency0.0130.0090.022
blankPlot0.0650.0020.067
colourHelices0.4390.0180.484
expandCollapseHelix0.0130.0010.014
logicalHelix0.6040.0180.624
logseq0.0010.0010.002
plotCovariance0.7600.0170.780
plotHelix0.8740.0370.913
readStructure0.0440.0040.048
structureMismatchScore0.0040.0020.008
unknottedGroups0.0320.0040.036
viennaToHelix0.0840.0030.087
writeHelix0.0040.0010.004