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CHECK report for R4RNA on malbec1

This page was generated on 2019-04-16 11:51:41 -0400 (Tue, 16 Apr 2019).

Package 1241/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
R4RNA 1.10.0
Daniel Lai
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/R4RNA
Branch: RELEASE_3_8
Last Commit: ba27cc1
Last Changed Date: 2018-10-30 11:41:59 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ 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: R4RNA
Version: 1.10.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:R4RNA.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings R4RNA_1.10.0.tar.gz
StartedAt: 2019-04-16 02:21:55 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:23:16 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 80.9 seconds
RetCode: 0
Status:  OK 
CheckDir: R4RNA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:R4RNA.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings R4RNA_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/R4RNA.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘1.10.0’
* 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 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/R4RNA.Rcheck/00check.log’
for details.



Installation output

R4RNA.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL R4RNA
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘R4RNA’ ...
** 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
* DONE (R4RNA)

Tests output


Example timings

R4RNA.Rcheck/R4RNA-Ex.timings

nameusersystemelapsed
R4RNA-package1.9560.0442.023
alignmentStatistics0.7680.0040.772
as.helix0.0000.0000.003
basepairFrequency0.0040.0040.011
blankPlot0.0600.0000.063
colourHelices0.4360.0080.447
expandCollapseHelix0.0160.0000.013
logicalHelix0.7400.0040.743
logseq0.0000.0000.001
plotCovariance0.8680.0040.873
plotHelix0.8840.0080.892
readStructure0.0480.0000.048
structureMismatchScore0.0040.0000.006
unknottedGroups0.0400.0000.038
viennaToHelix0.0840.0000.086
writeHelix0.0040.0000.004