Package: ExiMiR

Version: 2.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ExiMiR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ExiMiR_2.22.0.tar.gz

StartedAt: 2018-10-16 21:17:37 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 21:18:58 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 80.8 seconds

RetCode: 0

Status:  OK

CheckDir: ExiMiR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ExiMiR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ExiMiR_2.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ExiMiR.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 ‘ExiMiR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ExiMiR’ version ‘2.22.0’
* 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 ‘ExiMiR’ can be installed ... OK
* 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:
  ‘Biobase’
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘affyio’ ‘preprocessCore’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘Biobase’ ‘affy’ ‘limma’
  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
NormiR.bgcorrect.methods: no visible global function definition for
  ‘bgcorrect.methods’
NormiR.pmcorrect.methods: no visible global function definition for
  ‘mm’
NormiR.pmcorrect.methods: no visible global function definition for
  ‘pmcorrect.methods’
NormiR.summary.methods: no visible global function definition for
  ‘generateExprSet.methods’
ReadExi: no visible global function definition for ‘readTargets’
ReadExi: no visible global function definition for ‘read.maimages’
ReadExi: no visible global function definition for ‘readGAL’
ReadExi: no visible global function definition for ‘getLayout’
ReadExi: no visible global function definition for ‘head’
bg.boxplot: no visible global function definition for ‘boxplot’
bg.correct.miR: no visible global function definition for ‘new’
bg.correct.miR: no visible global function definition for ‘exprs’
bg.correct.miR: no visible global function definition for ‘se.exprs’
bg.correct.miR: no visible global function definition for
  ‘backgroundCorrect.matrix’
bg.correct.miR: no visible global function definition for ‘exprs<-’
bg.correct.miR: no visible global function definition for ‘se.exprs<-’
bg.correct.miR: no visible global function definition for
  ‘bgcorrect.methods’
bg.correct.miR: no visible global function definition for ‘bg.correct’
bg.hist: no visible global function definition for ‘hist’
bg.image: no visible global function definition for ‘image’
by.samples.curve: no visible global function definition for ‘plot’
by.samples.curve: no visible global function definition for ‘points’
by.samples.curve: no visible global function definition for ‘lines’
by.samples.figures: no visible global function definition for ‘dev.new’
by.samples.figures: no visible global function definition for ‘pdf’
by.samples.figures: no visible global function definition for ‘par’
by.samples.figures: no visible global function definition for ‘layout’
by.samples.figures: no visible global function definition for
  ‘dev.interactive’
by.samples.figures: no visible global function definition for ‘dev.off’
by.samples.legend: no visible global function definition for ‘plot’
by.samples.legend: no visible global function definition for ‘points’
by.samples.legend: no visible global function definition for ‘text’
by.samples.legend: no visible global function definition for ‘legend’
create.gal.env: no visible global function definition for ‘multiassign’
createAB: no visible global function definition for ‘new’
createAB: no visible global function definition for ‘runif’
createAB: no visible global function definition for ‘notes<-’
createAB: no visible global function definition for ‘notes’
createAB: no visible global function definition for ‘pData<-’
get.bg.ab: no visible global function definition for ‘new’
get.bg.ab: no visible global function definition for ‘se.exprs’
get.bg.ab: no visible global function definition for ‘exprs’
get.bg.ab: no visible global function definition for ‘cdfName’
get.bg.ab: no visible global function definition for ‘phenoData’
get.bg.ab: no visible global function definition for ‘annotation’
get.bg.ab: no visible global function definition for ‘protocolData’
get.bg.ab: no visible global function definition for ‘description’
get.bg.ab: no visible global function definition for ‘notes’
has.bg: no visible global function definition for ‘notes’
is.dual: no visible global function definition for ‘notes’
is.from.createAB: no visible global function definition for ‘notes’
make.gal.env: no visible global function definition for ‘readGAL’
make.gal.env: no visible global function definition for ‘getLayout’
meannorm: no visible global function definition for ‘exprs’
meannorm: no visible global function definition for ‘sampleNames’
mediannorm: no visible global function definition for ‘exprs’
mediannorm: no visible global function definition for ‘sampleNames’
mediannorm: no visible binding for global variable ‘median’
norm.miR: no visible global function definition for ‘getCdfInfo’
norm.miR: no visible global function definition for ‘new’
norm.miR: no visible global function definition for ‘exprs’
norm.miR: no visible global function definition for
  ‘normalizeQuantiles’
norm.miR: no visible global function definition for ‘normalize’
norm.miR: no visible global function definition for ‘exprs<-’
read.annotation.fromfile: no visible global function definition for
  ‘read.maimages’
spikeinnorm: no visible global function definition for ‘getCdfInfo’
spikeinnorm: no visible global function definition for ‘exprs’
spikeinnorm: no visible global function definition for ‘sampleNames’
spikeinnorm: no visible global function definition for ‘median’
spikeinnorm: no visible global function definition for ‘cor’
spikeinnorm: no visible binding for global variable ‘sd’
spikeinnorm: no visible global function definition for ‘dev.new’
spikeinnorm: no visible global function definition for ‘pdf’
spikeinnorm: no visible global function definition for ‘dev.cur’
spikeinnorm: no visible global function definition for ‘layout’
spikeinnorm: no visible global function definition for ‘par’
spikeinnorm: no visible global function definition for ‘matplot’
spikeinnorm: no visible global function definition for ‘rainbow’
spikeinnorm: no visible global function definition for ‘axis’
spikeinnorm: no visible global function definition for ‘plot’
spikeinnorm: no visible global function definition for ‘points’
spikeinnorm: no visible global function definition for ‘text’
spikeinnorm: no visible global function definition for ‘legend’
spikeinnorm: no visible global function definition for
  ‘dev.interactive’
spikeinnorm: no visible global function definition for ‘dev.off’
spikeinnorm: no visible global function definition for ‘rgb’
spikeinnorm: no visible global function definition for ‘heat.colors’
spikeinnorm: no visible global function definition for ‘image’
spikeinnorm: no visible binding for global variable ‘var’
spikeinnorm: no visible global function definition for ‘barplot’
spikeinnorm: no visible global function definition for ‘lm’
spikeinnorm: no visible global function definition for ‘predict’
spikeinnorm: no visible global function definition for ‘loess.smooth’
spikeinnorm: no visible global function definition for ‘approx’
summarize.miR: no visible global function definition for ‘mm’
summarize.miR: no visible global function definition for
  ‘computeExprSet’
Undefined global functions or variables:
  annotation approx axis backgroundCorrect.matrix barplot bg.correct
  bgcorrect.methods boxplot cdfName computeExprSet cor description
  dev.cur dev.interactive dev.new dev.off exprs exprs<-
  generateExprSet.methods getCdfInfo getLayout head heat.colors hist
  image layout legend lines lm loess.smooth matplot median mm
  multiassign new normalize normalizeQuantiles notes notes<- pData<-
  par pdf phenoData plot pmcorrect.methods points predict protocolData
  rainbow read.maimages readGAL readTargets rgb runif sampleNames sd
  se.exprs se.exprs<- text var
Consider adding
  importFrom("grDevices", "dev.cur", "dev.interactive", "dev.new",
             "dev.off", "heat.colors", "pdf", "rainbow", "rgb")
  importFrom("graphics", "axis", "barplot", "boxplot", "hist", "image",
             "layout", "legend", "lines", "matplot", "par", "plot",
             "points", "text")
  importFrom("methods", "new")
  importFrom("stats", "approx", "cor", "lm", "loess.smooth", "median",
             "predict", "runif", "sd", "var")
  importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
Examples with CPU or elapsed time > 5s
                user system elapsed
NormiR        16.478  0.148  16.797
summarize.miR 14.055  0.044  14.164
* 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-3.7-bioc/meat/ExiMiR.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 ExiMiR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ExiMiR’ ...
** 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 (ExiMiR)

name	user	system	elapsed
NormiR	16.478	0.148	16.797
ReadExi	0.001	0.000	0.001
bg.correct.miR	2.173	0.021	2.203
make.gal.env	0.001	0.000	0.001
norm.miR	0.606	0.053	0.663
summarize.miR	14.055	0.044	14.164