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CHECK report for R4RNA on riesling1

This page was generated on 2021-01-25 12:40:36 -0500 (Mon, 25 Jan 2021).

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 1412/1938HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
R4RNA 1.19.0
Daniel Lai
Snapshot Date: 2021-01-24 14:40:26 -0500 (Sun, 24 Jan 2021)
URL: https://git.bioconductor.org/packages/R4RNA
Branch: master
Last Commit: ba7bf7c
Last Changed Date: 2020-10-27 11:09:25 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 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
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ] OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: R4RNA
Version: 1.19.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:R4RNA.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings R4RNA_1.19.0.tar.gz
StartedAt: 2021-01-24 21:34:05 -0500 (Sun, 24 Jan 2021)
EndedAt: 2021-01-24 21:35:27 -0500 (Sun, 24 Jan 2021)
EllapsedTime: 81.6 seconds
RetCode: 0
Status:  OK  
CheckDir: R4RNA.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:R4RNA.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings R4RNA_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-bioc/meat/R4RNA.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'R4RNA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R4RNA' version '1.19.0'
* 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 '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
* 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
* 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 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 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 NOTE
See
  'D:/biocbuild/bbs-3.13-bioc/meat/R4RNA.Rcheck/00check.log'
for details.



Installation output

R4RNA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/bioc/src/contrib/R4RNA_1.19.0.tar.gz && rm -rf R4RNA.buildbin-libdir && mkdir R4RNA.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=R4RNA.buildbin-libdir R4RNA_1.19.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL R4RNA_1.19.0.zip && rm R4RNA_1.19.0.tar.gz R4RNA_1.19.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 38505  100 38505    0     0  18.3M      0 --:--:-- --:--:-- --:--:-- 18.3M

install for i386

* installing *source* package 'R4RNA' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'R4RNA'
    finding HTML links ... done
    R4RNA-package                           html  
REDIRECT:topic	 R4RNA -> R4RNA-package.html [ SUCCESS ]
REDIRECT:topic	 R4RNA-package -> R4RNA-package.html [ SUCCESS ]
    alignmentStatistics                     html  
REDIRECT:topic	 baseConservation -> alignmentStatistics.html [ SUCCESS ]
REDIRECT:topic	 basepairCanonical -> alignmentStatistics.html [ SUCCESS ]
REDIRECT:topic	 basepairConservation -> alignmentStatistics.html [ SUCCESS ]
REDIRECT:topic	 basepairCovariation -> alignmentStatistics.html [ SUCCESS ]
REDIRECT:topic	 helixCanonical -> alignmentStatistics.html [ SUCCESS ]
REDIRECT:topic	 helixConservation -> alignmentStatistics.html [ SUCCESS ]
REDIRECT:topic	 helixCovariation -> alignmentStatistics.html [ SUCCESS ]
REDIRECT:topic	 alignmentConservation -> alignmentStatistics.html [ SUCCESS ]
REDIRECT:topic	 alignmentCovariation -> alignmentStatistics.html [ SUCCESS ]
REDIRECT:topic	 alignmentCanonical -> alignmentStatistics.html [ SUCCESS ]
REDIRECT:topic	 alignmentPercentGaps -> alignmentStatistics.html [ SUCCESS ]
REDIRECT:file	 alignmentStatistics.html -> alignmentStatistics.html [ SUCCESS ]
    as.helix                                html  
REDIRECT:topic	 as.helix -> as.helix.html [ SUCCESS ]
REDIRECT:topic	 is.helix -> as.helix.html [ SUCCESS ]
REDIRECT:topic	 parseBracket -> as.helix.html [ SUCCESS ]
    basepairFrequency                       html  
REDIRECT:topic	 basepairFrequency -> basepairFrequency.html [ SUCCESS ]
    blankPlot                               html  
REDIRECT:topic	 blankPlot -> blankPlot.html [ SUCCESS ]
REDIRECT:topic	 maxHeight -> blankPlot.html [ SUCCESS ]
    colourHelices                           html  
REDIRECT:topic	 colourByCount -> colourHelices.html [ SUCCESS ]
REDIRECT:topic	 colourByValue -> colourHelices.html [ SUCCESS ]
REDIRECT:topic	 colourByConservation -> colourHelices.html [ SUCCESS ]
REDIRECT:topic	 colourByCovariation -> colourHelices.html [ SUCCESS ]
REDIRECT:topic	 colourByCanonical -> colourHelices.html [ SUCCESS ]
REDIRECT:topic	 colourByBasepairFrequency -> colourHelices.html [ SUCCESS ]
REDIRECT:topic	 colourByUnknottedGroups -> colourHelices.html [ SUCCESS ]
REDIRECT:topic	 defaultPalette -> colourHelices.html [ SUCCESS ]
REDIRECT:file	 colourHelices.html -> colourHelices.html [ SUCCESS ]
    expandCollapseHelix                     html  
REDIRECT:topic	 expandHelix -> expandCollapseHelix.html [ SUCCESS ]
REDIRECT:topic	 collapseHelix -> expandCollapseHelix.html [ SUCCESS ]
REDIRECT:file	 expandCollapseHelix.html -> expandCollapseHelix.html [ SUCCESS ]
    helix                                   html  
REDIRECT:topic	 helix -> helix.html [ SUCCESS ]
REDIRECT:topic	 fasta -> helix.html [ SUCCESS ]
REDIRECT:topic	 known -> helix.html [ SUCCESS ]
    logicalHelix                            html  
REDIRECT:topic	 isConflictingHelix -> logicalHelix.html [ SUCCESS ]
REDIRECT:topic	 isDuplicatingHelix -> logicalHelix.html [ SUCCESS ]
REDIRECT:topic	 isOverlappingHelix -> logicalHelix.html [ SUCCESS ]
REDIRECT:file	 logicalHelix.html -> logicalHelix.html [ SUCCESS ]
    logseq                                  html  
REDIRECT:topic	 logseq -> logseq.html [ SUCCESS ]
REDIRECT:topic	 logfloor -> logseq.html [ SUCCESS ]
REDIRECT:topic	 logceiling -> logseq.html [ SUCCESS ]
    plotCovariance                          html  
REDIRECT:topic	 plotCovariance -> plotCovariance.html [ SUCCESS ]
REDIRECT:topic	 plotDoubleCovariance -> plotCovariance.html [ SUCCESS ]
REDIRECT:topic	 plotOverlapCovariance -> plotCovariance.html [ SUCCESS ]
    plotHelix                               html  
REDIRECT:topic	 plotHelix -> plotHelix.html [ SUCCESS ]
REDIRECT:topic	 plotDoubleHelix -> plotHelix.html [ SUCCESS ]
REDIRECT:topic	 plotOverlapHelix -> plotHelix.html [ SUCCESS ]
REDIRECT:topic	 plotArcs -> plotHelix.html [ SUCCESS ]
REDIRECT:topic	 plotArc -> plotHelix.html [ SUCCESS ]
    readStructure                           html  
REDIRECT:topic	 readHelix -> readStructure.html [ SUCCESS ]
REDIRECT:topic	 readConnect -> readStructure.html [ SUCCESS ]
REDIRECT:topic	 readVienna -> readStructure.html [ SUCCESS ]
REDIRECT:topic	 readBpseq -> readStructure.html [ SUCCESS ]
REDIRECT:file	 readStructure.html -> readStructure.html [ SUCCESS ]
    structureMismatchScore                  html  
REDIRECT:topic	 structureMismatchScore -> structureMismatchScore.html [ SUCCESS ]
    unknottedGroups                         html  
REDIRECT:topic	 unknottedGroups -> unknottedGroups.html [ SUCCESS ]
    viennaToHelix                           html  
REDIRECT:topic	 viennaToHelix -> viennaToHelix.html [ SUCCESS ]
REDIRECT:topic	 helixToVienna -> viennaToHelix.html [ SUCCESS ]
REDIRECT:topic	 helixToConnect -> viennaToHelix.html [ SUCCESS ]
REDIRECT:topic	 helixToBpseq -> viennaToHelix.html [ SUCCESS ]
    writeHelix                              html  
REDIRECT:topic	 writeHelix -> writeHelix.html [ SUCCESS ]
** 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

install for x64

* installing *source* package 'R4RNA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'R4RNA' as R4RNA_1.19.0.zip
* DONE (R4RNA)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'R4RNA' successfully unpacked and MD5 sums checked

Tests output


Example timings

R4RNA.Rcheck/examples_i386/R4RNA-Ex.timings

nameusersystemelapsed
R4RNA-package1.210.031.31
alignmentStatistics0.420.000.42
as.helix000
basepairFrequency000
blankPlot0.050.000.04
colourHelices0.220.000.28
expandCollapseHelix000
logicalHelix0.360.000.39
logseq000
plotCovariance0.500.000.58
plotHelix0.760.020.86
readStructure0.040.000.03
structureMismatchScore000
unknottedGroups0.010.000.02
viennaToHelix0.050.000.07
writeHelix000

R4RNA.Rcheck/examples_x64/R4RNA-Ex.timings

nameusersystemelapsed
R4RNA-package1.000.101.16
alignmentStatistics0.420.000.42
as.helix000
basepairFrequency000
blankPlot0.060.000.07
colourHelices0.280.000.31
expandCollapseHelix000
logicalHelix0.500.000.55
logseq000
plotCovariance0.500.020.55
plotHelix0.520.000.57
readStructure0.030.000.04
structureMismatchScore0.000.020.01
unknottedGroups0.010.000.02
viennaToHelix0.070.010.07
writeHelix000