Package: R4RNA

Version: 1.6.0

Command: rm -rf R4RNA.buildbin-libdir R4RNA.Rcheck && mkdir R4RNA.buildbin-libdir R4RNA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=R4RNA.buildbin-libdir R4RNA_1.6.0.tar.gz >R4RNA.Rcheck\00install.out 2>&1 && cp R4RNA.Rcheck\00install.out R4RNA-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=R4RNA.buildbin-libdir --install="check:R4RNA-install.out" --force-multiarch --no-vignettes --timings R4RNA_1.6.0.tar.gz

StartedAt: 2018-04-12 02:26:38 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:28:26 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 108.6 seconds

RetCode: 0

Status:  OK

CheckDir: R4RNA.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf R4RNA.buildbin-libdir R4RNA.Rcheck && mkdir R4RNA.buildbin-libdir R4RNA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=R4RNA.buildbin-libdir R4RNA_1.6.0.tar.gz >R4RNA.Rcheck\00install.out 2>&1 && cp R4RNA.Rcheck\00install.out R4RNA-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=R4RNA.buildbin-libdir --install="check:R4RNA-install.out" --force-multiarch --no-vignettes --timings R4RNA_1.6.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/R4RNA.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.6.0'
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... 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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/R4RNA.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'R4RNA' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'R4RNA'
    finding HTML links ... done
    R4RNA-package                           html  
    alignmentStatistics                     html  
    as.helix                                html  
    basepairFrequency                       html  
    blankPlot                               html  
    colourHelices                           html  
    expandCollapseHelix                     html  
    helix                                   html  
    logicalHelix                            html  
    logseq                                  html  
    plotCovariance                          html  
    plotHelix                               html  
    readStructure                           html  
    structureMismatchScore                  html  
    unknottedGroups                         html  
    viennaToHelix                           html  
    writeHelix                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'R4RNA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'R4RNA' as R4RNA_1.6.0.zip
* DONE (R4RNA)
In R CMD INSTALL
In R CMD INSTALL