Multiple platform build/check report for BioC 3.6 - CHECK report for htSeqTools on tokay1

Package: htSeqTools

Version: 1.26.0

Command: rm -rf htSeqTools.buildbin-libdir htSeqTools.Rcheck && mkdir htSeqTools.buildbin-libdir htSeqTools.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=htSeqTools.buildbin-libdir htSeqTools_1.26.0.tar.gz >htSeqTools.Rcheck\00install.out 2>&1 && cp htSeqTools.Rcheck\00install.out htSeqTools-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=htSeqTools.buildbin-libdir --install="check:htSeqTools-install.out" --force-multiarch --no-vignettes --timings htSeqTools_1.26.0.tar.gz

StartedAt: 2018-04-12 00:45:19 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:50:20 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 301.1 seconds

RetCode: 0

Status: WARNINGS

CheckDir: htSeqTools.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf htSeqTools.buildbin-libdir htSeqTools.Rcheck && mkdir htSeqTools.buildbin-libdir htSeqTools.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=htSeqTools.buildbin-libdir htSeqTools_1.26.0.tar.gz >htSeqTools.Rcheck\00install.out 2>&1 && cp htSeqTools.Rcheck\00install.out htSeqTools-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=htSeqTools.buildbin-libdir --install="check:htSeqTools-install.out" --force-multiarch --no-vignettes --timings htSeqTools_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/htSeqTools.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 'htSeqTools/DESCRIPTION' ... OK
* this is package 'htSeqTools' version '1.26.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'multicore'

Depends: includes the non-default packages:
  'BiocGenerics' 'Biobase' 'S4Vectors' 'IRanges' 'MASS' 'BSgenome'
  'GenomeInfoDb' 'GenomicRanges'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'htSeqTools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods'
A package should be listed in only one of these fields.
* 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 ... NOTE
'library' or 'require' call to 'parallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'Biobase'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'S4Vectors:::decodeRle'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PeakLocationBase: no visible global function definition for
  'nclass.Sturges'
PeakLocationBase: no visible global function definition for 'hist'
PeakLocationBase: no visible global function definition for 'par'
PeakLocationBase: no visible global function definition for 'segments'
PeakLocationBase: no visible global function definition for 'text'
fdrEnrichedCounts : getNBinomParams : myLikelihood: no visible global
  function definition for 'dnbinom'
fdrEnrichedCounts : getNBinomParams : myLikelihood: no visible global
  function definition for 'dmultinom'
fdrEnrichedCounts : getNBinomParams : mynlminb: no visible global
  function definition for 'nlminb'
fdrEnrichedCounts: no visible global function definition for 'isoreg'
fdrEnrichedCounts: no visible global function definition for 'dnbinom'
getGrid: no visible global function definition for 'approxfun'
plotChrRegions: no visible global function definition for 'segments'
plotChrRegions: no visible global function definition for 'text'
plotChrRegions: no visible global function definition for 'rect'
plotminHeight: no visible global function definition for 'isoreg'
plotminHeight: no visible global function definition for 'approxfun'
plotminHeight: no visible global function definition for 'abline'
plotminHeight: no visible global function definition for 'par'
plotminHeight: no visible global function definition for 'points'
plotminHeight: no visible global function definition for 'axis'
plotminHeight: no visible global function definition for 'legend'
randomHitsWindow: no visible global function definition for 'rmultinom'
randomHitsWindow: no visible global function definition for 'runif'
rowLogRegLRT: no visible global function definition for 'pchisq'
rowLogRegLRT : <anonymous>: no visible global function definition for
  'chisq.test'
rowLogRegLRT: no visible global function definition for 'p.adjust'
stdPeakLocationBase: no visible global function definition for 'hist'
stdPeakLocationBase: no visible global function definition for 'par'
stdPeakLocationBase: no visible global function definition for
  'segments'
stdPeakLocationBase: no visible global function definition for 'text'
cmds,list: no visible global function definition for 'as.dist'
cmds,list: no visible global function definition for 'cmdscale'
cmds,list: no visible global function definition for 'dist'
cmdsFit,matrix: no visible global function definition for 'cmdscale'
cmdsFit,matrix: no visible global function definition for 'as.dist'
cmdsFit,matrix: no visible global function definition for 'dist'
countHitsWindow,GRanges: possible error in countHitsWindow(x,
  chrLengths = chrLengths, windowSize = windowSize): unused argument
  (chrLengths = chrLengths)
countHitsWindow,GRanges: no visible binding for global variable
  'chrLengths'
enrichedPeaks,RangedData-IRangesList-IRangesList: no visible global
  function definition for 'pvec'
enrichedPeaks,RangedData-IRangesList-missing: no visible global
  function definition for 'pvec'
enrichedRegions,RangedData-missing-missing-ANY-ANY: no visible global
  function definition for 'pbinom'
enrichedRegions,RangedData-missing-missing-ANY-ANY: no visible global
  function definition for 'p.adjust'
extendRanges,GRanges: possible error in extendRanges(x, seqLen =
  seqLen, chrLength = chrLength, mc.cores = mc.cores): unused argument
  (chrLength = chrLength)
extendRanges,GRanges: no visible binding for global variable
  'chrLength'
extendRanges,GRangesList: possible error in extendRanges(x, seqLen =
  seqLen, chrLength = chrLength, mc.cores = mc.cores): unused argument
  (chrLength = chrLength)
extendRanges,GRangesList: no visible binding for global variable
  'chrLength'
findPeakHeight,RangedData-IRangesList-IRangesList: no visible global
  function definition for 'pvec'
findPeakHeight,RangedData-IRangesList-IRangesList: no visible global
  function definition for 'isoreg'
findPeakHeight,RangedData-IRangesList-IRangesList: no visible global
  function definition for 'approxfun'
giniCoverage,RangedData-ANY-ANY-ANY-missing-integer : lorenzC :
  plot.Lc: no visible global function definition for 'abline'
giniCoverage,RangedData-ANY-ANY-ANY-missing-integer : plotRes: no
  visible global function definition for 'par'
listOverlap,character-character-character-character: no visible global
  function definition for 'glm'
listOverlap,character-character-character-character: no visible global
  function definition for 'anova'
listOverlap,character-character-missing-character: no visible global
  function definition for 'chisq.test'
listOverlap,factor-character-missing-missing: no visible global
  function definition for 'chisq.test'
plot,cmdsFit-ANY: no visible global function definition for 'text'
plot,gridCover-ANY: no visible global function definition for 'text'
plot,gridCover-ANY: no visible global function definition for 'par'
plotMeanCoverage,RleList-RangedData: no visible global function
  definition for 'loess'
ssdCoverage,IRangesList: no visible global function definition for
  'weighted.mean'
Undefined global functions or variables:
  abline anova approxfun as.dist axis chisq.test chrLength chrLengths
  cmdscale dist dmultinom dnbinom glm hist isoreg legend loess
  nclass.Sturges nlminb p.adjust par pbinom pchisq points pvec rect
  rmultinom runif segments text weighted.mean
Consider adding
  importFrom("grDevices", "nclass.Sturges")
  importFrom("graphics", "abline", "axis", "hist", "legend", "par",
             "points", "rect", "segments", "text")
  importFrom("stats", "anova", "approxfun", "as.dist", "chisq.test",
             "cmdscale", "dist", "dmultinom", "dnbinom", "glm", "isoreg",
             "loess", "nlminb", "p.adjust", "pbinom", "pchisq",
             "rmultinom", "runif", "weighted.mean")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'gridCover,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
Examples with CPU or elapsed time > 5s
             user system elapsed
giniCoverage 5.72    0.2    5.92
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
giniCoverage 6.57   0.16    6.73
* 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 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/htSeqTools.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'htSeqTools' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'htSeqTools'
    finding HTML links ... done
    alignPeaks                              html  
    cmds                                    html  
    cmdsFit-class                           html  
    cmdsFit                                 html  
    countHitsWindow                         html  
    coverageDiff                            html  
    enrichedChrRegions                      html  
    enrichedPeaks                           html  
    enrichedRegions                         html  
    extendRanges                            html  
    fdrEnrichedCounts                       html  
    filterDuplReads                         html  
    findPeakHeight                          html  
    giniCoverage                            html  
    gridCover-class                         html  
    htSample                                html  
    islandCounts                            html  
    listOverlap                             html  
    mergeRegions                            html  
    plot-methods                            html  
    plotChrRegions                          html  
    regionsCoverage                         html  
    rowLogRegLRT                            html  
    ssdCoverage                             html  
    stdPeakLocation                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'htSeqTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'htSeqTools' as htSeqTools_1.26.0.zip
* DONE (htSeqTools)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for htSeqTools on tokay1

Summary

Command output

Installation output

Tests output

Example timings