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BioC 3.4: CHECK report for htSeqTools on malbec1

This page was generated on 2017-04-15 16:10:30 -0400 (Sat, 15 Apr 2017).

Package 603/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
htSeqTools 1.22.0
Oscar Reina
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/htSeqTools
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: htSeqTools
Version: 1.22.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings htSeqTools_1.22.0.tar.gz
StartedAt: 2017-04-14 23:14:02 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:17:01 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 178.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: htSeqTools.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings htSeqTools_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/htSeqTools.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘htSeqTools/DESCRIPTION’ ... OK
* this is package ‘htSeqTools’ version ‘1.22.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
giniCoverage 5.524   0.02   5.548
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/htSeqTools.Rcheck/00check.log’
for details.


htSeqTools.Rcheck/00install.out:

* installing *source* package ‘htSeqTools’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (htSeqTools)

htSeqTools.Rcheck/htSeqTools-Ex.timings:

nameusersystemelapsed
alignPeaks0.1040.0120.114
cmds1.8920.0081.898
cmdsFit-class000
cmdsFit0.0000.0000.001
countHitsWindow0.0360.0000.034
coverageDiff0.0840.0040.087
enrichedChrRegions1.1600.0161.175
enrichedPeaks0.6280.0040.633
enrichedRegions0.1880.0000.187
extendRanges0.1160.0000.117
fdrEnrichedCounts0.1200.0040.122
filterDuplReads0.2400.0000.242
findPeakHeight0.8160.0000.815
giniCoverage5.5240.0205.548
gridCover-class000
htSample0.3360.0000.335
islandCounts0.1880.0000.188
listOverlap0.0040.0000.005
mergeRegions0.0400.0000.039
plot-methods0.0000.0000.001
plotChrRegions0.0040.0040.010
regionsCoverage0.0000.0000.001
rowLogRegLRT0.0000.0000.002
ssdCoverage0.2720.0080.279
stdPeakLocation0.0640.0000.063