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CHECK report for quantsmooth on merida2

This page was generated on 2018-10-17 08:47:01 -0400 (Wed, 17 Oct 2018).

Package 1163/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
quantsmooth 1.46.0
Jan Oosting
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/quantsmooth
Branch: RELEASE_3_7
Last Commit: 9e435f4
Last Changed Date: 2018-04-30 10:35:05 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: quantsmooth
Version: 1.46.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:quantsmooth.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings quantsmooth_1.46.0.tar.gz
StartedAt: 2018-10-16 23:27:28 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 23:28:23 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 54.8 seconds
RetCode: 0
Status:  OK 
CheckDir: quantsmooth.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:quantsmooth.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings quantsmooth_1.46.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/quantsmooth.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘quantsmooth/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘quantsmooth’ version ‘1.46.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘quantsmooth’ 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
* 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
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getChrombands: no visible global function definition for ‘data’
drawSimpleChrom: no visible global function definition for ‘rect’
drawSimpleChrom: no visible global function definition for ‘lines’
drawSimpleChrom: no visible global function definition for ‘yinch’
drawSimpleChrom: no visible global function definition for ‘symbols’
drawSimpleChrom: no visible global function definition for ‘xinch’
grid.chromosome: no visible global function definition for ‘gray’
grid.chromosome: no visible global function definition for
  ‘pushViewport’
grid.chromosome: no visible global function definition for ‘viewport’
grid.chromosome: no visible global function definition for ‘grid.rect’
grid.chromosome: no visible global function definition for ‘gpar’
grid.chromosome: no visible global function definition for
  ‘grid.circle’
grid.chromosome: no visible global function definition for ‘unit’
grid.chromosome: no visible global function definition for ‘grid.text’
grid.chromosome: no visible global function definition for
  ‘popViewport’
lengthChromosome: no visible global function definition for ‘aggregate’
paintCytobands: no visible global function definition for ‘gray’
paintCytobands: no visible global function definition for ‘rect’
paintCytobands: no visible global function definition for ‘yinch’
paintCytobands: no visible global function definition for ‘symbols’
paintCytobands: no visible global function definition for ‘text’
paintCytobands: no visible global function definition for ‘xinch’
plotSmoothed: no visible global function definition for ‘plot’
plotSmoothed: no visible global function definition for ‘abline’
plotSmoothed: no visible global function definition for ‘points’
plotSmoothed: no visible global function definition for ‘lines’
prepareGenomePlot: no visible global function definition for ‘par’
prepareGenomePlot: no visible global function definition for ‘plot’
prepareGenomePlot: no visible global function definition for ‘axis’
prepareGenomePlot: no visible global function definition for ‘lines’
qs.grid.semicircle: no visible global function definition for
  ‘grid.polygon’
qs.semicircle: no visible global function definition for ‘polygon’
qs.semicircle: no visible global function definition for ‘lines’
Undefined global functions or variables:
  abline aggregate axis data gpar gray grid.circle grid.polygon
  grid.rect grid.text lines par plot points polygon popViewport
  pushViewport rect symbols text unit viewport xinch yinch
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "lines", "par", "plot",
             "points", "polygon", "rect", "symbols", "text", "xinch",
             "yinch")
  importFrom("stats", "aggregate")
  importFrom("utils", "data")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/quantsmooth.Rcheck/00check.log’
for details.



Installation output

quantsmooth.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL quantsmooth
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘quantsmooth’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (quantsmooth)

Tests output


Example timings

quantsmooth.Rcheck/quantsmooth-Ex.timings

nameusersystemelapsed
drawSimpleChrom0.0110.0020.012
getChangedRegions0.1120.0130.124
getLambdaMin0.4130.0450.460
grid.chromosome0.0530.0020.055
lengthChromosome0.0840.0060.756
numericCHR0.0030.0000.004
paintCytobands0.0660.0030.069
plotSmoothed0.0910.0080.100
position2Cytoband0.0550.0020.058
quantsmooth0.0130.0030.017
quantsmooth.cv0.0260.0030.029
quantsmooth.seg0.0060.0020.007