Package: htSeqTools

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:htSeqTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings htSeqTools_1.30.0.tar.gz

StartedAt: 2019-04-16 00:36:48 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:40:34 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 226.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: htSeqTools.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:htSeqTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings htSeqTools_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/htSeqTools.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘htSeqTools/DESCRIPTION’ ... OK
* this is package ‘htSeqTools’ version ‘1.30.0’
* 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 ... WARNING
Found the following significant warnings:
  Note: possible error in 'countHitsWindow(x, chrLengths = chrLengths, ': unused argument (chrLengths = chrLengths) 
  Note: possible error in 'extendRanges(x, seqLen = seqLen, ': unused argument (chrLength = chrLength) 
See ‘/Users/biocbuild/bbs-3.8-bioc/meat/htSeqTools.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 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
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’
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’
Undefined global functions or variables:
  chrLength chrLengths pvec
* 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 sizes of PDF files under ‘inst/doc’ ... 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 6.185  0.114    6.33
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/htSeqTools.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL htSeqTools
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘htSeqTools’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'countHitsWindow(x, chrLengths = chrLengths, ': unused argument (chrLengths = chrLengths) 
Note: possible error in 'countHitsWindow(x, chrLengths = chrLengths, ': unused argument (chrLengths = chrLengths) 
Note: possible error in 'countHitsWindow(x, chrLengths = chrLengths, ': unused argument (chrLengths = chrLengths) 
Note: possible error in 'extendRanges(x, seqLen = seqLen, ': unused argument (chrLength = chrLength) 
Note: possible error in 'extendRanges(x, seqLen = seqLen, ': unused argument (chrLength = chrLength) 
Note: possible error in 'extendRanges(x, seqLen = seqLen, ': unused argument (chrLength = chrLength) 
Note: possible error in 'extendRanges(x, seqLen = seqLen, ': unused argument (chrLength = chrLength) 
Note: possible error in 'extendRanges(x, seqLen = seqLen, ': unused argument (chrLength = chrLength) 
Note: possible error in 'extendRanges(x, seqLen = seqLen, ': unused argument (chrLength = chrLength) 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (htSeqTools)

name	user	system	elapsed
alignPeaks	0.256	0.021	0.278
cmds	1.653	0.106	1.779
cmdsFit-class	0.001	0.000	0.002
cmdsFit	0.000	0.000	0.001
countHitsWindow	0.095	0.000	0.100
coverageDiff	0.208	0.001	0.210
enrichedChrRegions	2.384	0.184	2.644
enrichedPeaks	1.113	0.026	1.150
enrichedRegions	0.289	0.001	0.290
extendRanges	0.191	0.001	0.193
fdrEnrichedCounts	0.130	0.003	0.132
filterDuplReads	0.276	0.004	0.281
findPeakHeight	1.251	0.006	1.267
giniCoverage	6.185	0.114	6.330
gridCover-class	0	0	0
htSample	0.377	0.024	0.402
islandCounts	0.408	0.006	0.419
listOverlap	0.006	0.000	0.006
mergeRegions	0.054	0.005	0.060
plot-methods	0	0	0
plotChrRegions	0.014	0.001	0.015
regionsCoverage	0	0	0
rowLogRegLRT	0.003	0.000	0.003
ssdCoverage	0.306	0.033	0.341
stdPeakLocation	0.244	0.014	0.261