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CHECK report for MmPalateMiRNA on merida1

This page was generated on 2019-04-16 11:56:09 -0400 (Tue, 16 Apr 2019).

Package 986/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MmPalateMiRNA 1.32.0
Guy Brock
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/MmPalateMiRNA
Branch: RELEASE_3_8
Last Commit: c7088b6
Last Changed Date: 2018-10-30 11:41:48 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  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: MmPalateMiRNA
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MmPalateMiRNA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MmPalateMiRNA_1.32.0.tar.gz
StartedAt: 2019-04-16 01:22:32 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:23:34 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 62.3 seconds
RetCode: 0
Status:  OK 
CheckDir: MmPalateMiRNA.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:MmPalateMiRNA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MmPalateMiRNA_1.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/MmPalateMiRNA.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 ‘MmPalateMiRNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MmPalateMiRNA’ version ‘1.32.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Biobase’ ‘xtable’ ‘limma’ ‘statmod’ ‘lattice’ ‘vsn’
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 ‘MmPalateMiRNA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘limma’ ‘lattice’ ‘Biobase’
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
Packages in Depends field not imported from:
  ‘methods’ ‘statmod’ ‘vsn’ ‘xtable’
  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
clustPlot: no visible global function definition for ‘par’
clustPlot: no visible global function definition for ‘plot’
clustPlot: no visible global function definition for ‘axis’
clustPlot: no visible global function definition for ‘lines’
clustPlot: no visible global function definition for ‘legend’
fixOutliers : <anonymous>: no visible global function definition for
  ‘sd’
imputeKNN: no visible global function definition for ‘sd’
imputeKNN: no visible global function definition for ‘cor’
MADvsMedianPlot,list : <anonymous>: no visible global function
  definition for ‘RG.MA’
MADvsMedianPlot,list : <anonymous>: no visible global function
  definition for ‘assayData’
MADvsMedianPlot,list : <anonymous>: no visible binding for global
  variable ‘mad’
MADvsMedianPlot,list : <anonymous>: no visible binding for global
  variable ‘median’
MADvsMedianPlot,list: no visible global function definition for ‘stack’
MADvsMedianPlot,list : <anonymous>: no visible global function
  definition for ‘pData’
MADvsMedianPlot,list : <anonymous>: no visible global function
  definition for ‘featureData’
MAplot,MAList: no visible global function definition for ‘stack’
MAplot,NChannelSet: no visible global function definition for
  ‘assayData’
MAplot,NChannelSet: no visible global function definition for ‘stack’
checkOutliers,RGList: no visible binding for global variable ‘sd’
densityplot,RGList-missing: no visible global function definition for
  ‘as.formula’
densityplot,list-missing : <anonymous>: no visible global function
  definition for ‘RG.MA’
densityplot,list-missing : <anonymous>: no visible global function
  definition for ‘assayData’
densityplot,list-missing : <anonymous>: no visible global function
  definition for ‘pData’
densityplot,list-missing : <anonymous>: no visible global function
  definition for ‘featureData’
densityplot,list-missing: no visible global function definition for
  ‘as.formula’
levelplot,RGList-missing: no visible global function definition for
  ‘median’
levelplot,list-missing : <anonymous>: no visible global function
  definition for ‘RG.MA’
levelplot,list-missing : <anonymous>: no visible global function
  definition for ‘assayData’
levelplot,list-missing: no visible global function definition for
  ‘median’
Undefined global functions or variables:
  RG.MA as.formula assayData axis cor featureData legend lines mad
  median pData par plot sd stack
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "par", "plot")
  importFrom("stats", "as.formula", "cor", "mad", "median", "sd")
  importFrom("utils", "stack")
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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/MmPalateMiRNA.Rcheck/00check.log’
for details.



Installation output

MmPalateMiRNA.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MmPalateMiRNA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘MmPalateMiRNA’ ...
** 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 (MmPalateMiRNA)

Tests output


Example timings

MmPalateMiRNA.Rcheck/MmPalateMiRNA-Ex.timings

nameusersystemelapsed
MADvsMedianPlot1.5080.0541.570
MAplot0.3940.0290.425
PalateData0.0620.0070.068
checkMVs0.1760.0070.188
checkOutliers2.3880.0132.433
clustPlot0.0910.0020.093
densityplot0.7460.0300.794
filterArray0.1010.0110.113
fixMVs0.1810.0090.194
fixOutliers2.5290.0132.578
imputeKNN0.0100.0010.011
levelplot0.3950.0300.432