Package: qusage

Version: 2.16.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:qusage.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qusage_2.16.1.tar.gz

StartedAt: 2019-04-16 02:09:34 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:11:29 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 115.4 seconds

RetCode: 0

Status:  OK

CheckDir: qusage.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:qusage.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qusage_2.16.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/qusage.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 ‘qusage/DESCRIPTION’ ... OK
* this is package ‘qusage’ version ‘2.16.1’
* 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 ‘qusage’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
absoluteTest : <anonymous>: no visible global function definition for
  ‘pchisq’
absoluteTest.genePvals: no visible global function definition for ‘qt’
absoluteTest.genePvals: no visible global function definition for
  ‘approx’
absoluteTest.genePvals: no visible global function definition for ‘dt’
absoluteTest.genePvals: no visible global function definition for
  ‘pnorm’
absoluteTest.genePvals: no visible global function definition for ‘pt’
absoluteTest.genePvalsFAST : <anonymous>: no visible global function
  definition for ‘pt’
aggregateGeneSet: no visible global function definition for ‘qt’
aggregateGeneSet : <anonymous>: no visible global function definition
  for ‘dt’
calcPCor: no visible global function definition for ‘model.matrix’
calcPCor: no visible global function definition for ‘formula’
calcPCor : <anonymous>: no visible global function definition for ‘cov’
calcVIF: no visible global function definition for ‘model.matrix’
calcVIF: no visible global function definition for ‘formula’
calcVIF : <anonymous>: no visible global function definition for ‘cov’
combinePDFs : <anonymous> : <anonymous>: no visible global function
  definition for ‘approx’
combinePDFs : <anonymous>: no visible global function definition for
  ‘approx’
compareTwoDistsFaster: no visible global function definition for
  ‘runif’
getExAbs: no visible global function definition for ‘approx’
homogeneityScore : <anonymous>: no visible global function definition
  for ‘pchisq’
makeComparison: no visible global function definition for
  ‘model.matrix’
makeComparison: no visible global function definition for ‘formula’
multi_conv : <anonymous>: no visible global function definition for
  ‘fft’
multi_conv: no visible global function definition for ‘fft’
plotCIs: no visible global function definition for ‘p.adjust’
plotCIs: no visible global function definition for ‘par’
plotCIs: no visible global function definition for ‘rgb’
plotCIs: no visible global function definition for ‘abline’
plotCIs: no visible global function definition for ‘gray’
plotCIs: no visible global function definition for ‘axis’
plotCIs: no visible global function definition for ‘text’
plotCIs: no visible global function definition for ‘arrows’
plotCIs: no visible global function definition for ‘points’
plotCIs: no visible global function definition for ‘strwidth’
plotCIs: no visible global function definition for ‘strheight’
plotCIs: no visible global function definition for ‘polygon’
plotCIs: no visible global function definition for ‘box’
plotCIsGenes : <anonymous>: no visible global function definition for
  ‘qt’
plotCIsGenes: no visible global function definition for ‘dt’
plotCIsGenes: no visible global function definition for ‘par’
plotCIsGenes: no visible global function definition for ‘abline’
plotCIsGenes: no visible global function definition for ‘gray’
plotCIsGenes: no visible global function definition for ‘polygon’
plotCIsGenes: no visible global function definition for ‘grey’
plotCIsGenes: no visible global function definition for ‘points’
plotCIsGenes: no visible global function definition for ‘arrows’
plotCIsGenes: no visible global function definition for ‘axis’
plotCIsGenes: no visible global function definition for ‘text’
plotCIsGenes: no visible global function definition for ‘box’
plotCombinedPDF: no visible global function definition for ‘par’
plotCombinedPDF: no visible global function definition for ‘abline’
plotCombinedPDF: no visible global function definition for ‘lines’
plotDensityCurves: no visible global function definition for ‘par’
plotDensityCurves: no visible global function definition for ‘abline’
plotDensityCurves: no visible global function definition for ‘lines’
plotGeneSetDistributions: no visible global function definition for
  ‘layout’
plotGeneSetDistributions: no visible global function definition for
  ‘par’
plotGeneSetDistributions: no visible global function definition for
  ‘frame’
plotGeneSetDistributions: no visible global function definition for
  ‘text’
plotGeneSetDistributions: no visible global function definition for
  ‘axis’
plotGeneSetDistributions: no visible global function definition for
  ‘dt’
plotGeneSetDistributions: no visible global function definition for
  ‘quantile’
plotGeneSetDistributions: no visible global function definition for
  ‘rect’
plotGeneSetDistributions: no visible global function definition for
  ‘col2rgb’
plotGeneSetDistributions: no visible global function definition for
  ‘rainbow’
plotGeneSetDistributions: no visible global function definition for
  ‘colorRamp’
plotGeneSetDistributions: no visible global function definition for
  ‘rgb’
plotGeneSetDistributions: no visible global function definition for
  ‘approx’
plotGeneSetDistributions: no visible global function definition for
  ‘lines’
plotGeneSetDistributions: no visible global function definition for
  ‘abline’
qgen: no visible global function definition for ‘median’
qgen: no visible global function definition for ‘model.matrix’
qgen: no visible global function definition for ‘formula’
qgen: no visible global function definition for ‘residuals’
qgen: no visible global function definition for ‘lm’
qgen: no visible global function definition for ‘setNames’
qsTable: no visible global function definition for ‘p.adjust’
twoCurve.pVal : <anonymous>: no visible global function definition for
  ‘approx’
weighted_conv: no visible global function definition for ‘approx’
weighted_conv: no visible global function definition for ‘convolve’
Undefined global functions or variables:
  abline approx arrows axis box col2rgb colorRamp convolve cov dt fft
  formula frame gray grey layout lines lm median model.matrix p.adjust
  par pchisq pnorm points polygon pt qt quantile rainbow rect residuals
  rgb runif setNames strheight strwidth text
Consider adding
  importFrom("grDevices", "col2rgb", "colorRamp", "gray", "grey",
             "rainbow", "rgb")
  importFrom("graphics", "abline", "arrows", "axis", "box", "frame",
             "layout", "lines", "par", "points", "polygon", "rect",
             "strheight", "strwidth", "text")
  importFrom("stats", "approx", "convolve", "cov", "dt", "fft",
             "formula", "lm", "median", "model.matrix", "p.adjust",
             "pchisq", "pnorm", "pt", "qt", "quantile", "residuals",
             "runif", "setNames")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: GeneSets.Rd:20: Dropping empty section \format
* 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
qgen 23.761  0.673  24.968
* 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/qusage.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 qusage
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘qusage’ ...
** R
** data
** inst
** 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 (qusage)

name	user	system	elapsed
aggregateGeneSet	0.137	0.021	0.159
calcVIF	0.236	0.023	0.266
combinePDFs	2.327	0.190	2.567
getXcoords	0.192	0.018	0.210
makeComparison	0.008	0.002	0.010
pVal	0.588	0.026	0.615
plotCIs	1.123	0.043	1.216
plotCIsGenes	0.192	0.009	0.202
plotCombinedPDF	3.527	0.085	3.738
plotDensityCurves	0.266	0.020	0.289
plotGeneSetDistributions	2.317	0.088	2.458
qgen	23.761	0.673	24.968
qsTable	0.943	0.050	0.995
qusage	0.810	0.029	0.844