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CHECK report for htSeqTools on merida1

This page was generated on 2019-04-16 12:10:41 -0400 (Tue, 16 Apr 2019).

Package 738/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
htSeqTools 1.30.0
Oscar Reina
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/htSeqTools
Branch: RELEASE_3_8
Last Commit: 613ed18
Last Changed Date: 2018-10-30 11:42:09 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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### Running 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
###
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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.



Installation output

htSeqTools.Rcheck/00install.out

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###
### Running command:
###
###   /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)

Tests output


Example timings

htSeqTools.Rcheck/htSeqTools-Ex.timings

nameusersystemelapsed
alignPeaks0.2560.0210.278
cmds1.6530.1061.779
cmdsFit-class0.0010.0000.002
cmdsFit0.0000.0000.001
countHitsWindow0.0950.0000.100
coverageDiff0.2080.0010.210
enrichedChrRegions2.3840.1842.644
enrichedPeaks1.1130.0261.150
enrichedRegions0.2890.0010.290
extendRanges0.1910.0010.193
fdrEnrichedCounts0.1300.0030.132
filterDuplReads0.2760.0040.281
findPeakHeight1.2510.0061.267
giniCoverage6.1850.1146.330
gridCover-class000
htSample0.3770.0240.402
islandCounts0.4080.0060.419
listOverlap0.0060.0000.006
mergeRegions0.0540.0050.060
plot-methods000
plotChrRegions0.0140.0010.015
regionsCoverage000
rowLogRegLRT0.0030.0000.003
ssdCoverage0.3060.0330.341
stdPeakLocation0.2440.0140.261