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CHECK report for quantsmooth on malbec1

This page was generated on 2020-04-15 12:04:44 -0400 (Wed, 15 Apr 2020).

Package 1350/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
quantsmooth 1.52.0
Jan Oosting
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/quantsmooth
Branch: RELEASE_3_10
Last Commit: 78d969a
Last Changed Date: 2019-10-29 13:07:43 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: quantsmooth
Version: 1.52.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:quantsmooth.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings quantsmooth_1.52.0.tar.gz
StartedAt: 2020-04-15 00:20:26 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:21:15 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 49.1 seconds
RetCode: 0
Status:  OK 
CheckDir: quantsmooth.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:quantsmooth.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings quantsmooth_1.52.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/quantsmooth.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘1.52.0’
* 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 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/quantsmooth.Rcheck/00check.log’
for details.



Installation output

quantsmooth.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL quantsmooth
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘quantsmooth’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (quantsmooth)

Tests output


Example timings

quantsmooth.Rcheck/quantsmooth-Ex.timings

nameusersystemelapsed
drawSimpleChrom0.0080.0000.007
getChangedRegions0.0720.0080.077
getLambdaMin0.2960.0160.311
grid.chromosome0.0360.0040.042
lengthChromosome0.0880.0080.492
numericCHR0.0000.0000.001
paintCytobands0.0840.0000.085
plotSmoothed0.1040.0000.106
position2Cytoband0.0560.0000.055
quantsmooth0.0120.0040.014
quantsmooth.cv0.0320.0040.034
quantsmooth.seg0.0080.0000.007