BioC 3.3: CHECK report for MEAL on morelia

Package: MEAL

Version: 1.1.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MEAL_1.1.6.tar.gz

StartedAt: 2016-04-21 04:40:08 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 04:51:21 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 673.4 seconds

RetCode: 0

Status:  OK

CheckDir: MEAL.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MEAL_1.1.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/MEAL.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MEAL/DESCRIPTION’ ... OK
* this is package ‘MEAL’ version ‘1.1.6’
* 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 ‘MEAL’ can be installed ... [30s/32s] 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 loading without being on the library search path ... 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
DAPipeline: no visible global function definition for 'model.matrix'
DAProbe: no visible global function definition for 'contrasts'
DAProbe: no visible global function definition for 'qt'
DARegionAnalysis: no visible global function definition for
  'model.matrix'
DARegionAnalysis: no visible global function definition for 'prcomp'
SNPsforCPG: no visible global function definition for 'formula'
correlationMethExprs: no visible global function definition for
  'p.adjust'
createModel: no visible global function definition for 'model.matrix'
createModel: no visible global function definition for 'formula'
explainedVariance: no visible global function definition for 'lm'
explainedVariance: no visible global function definition for 'formula'
explainedVariance : <anonymous>: no visible global function definition
  for 'lm'
explainedVariance : <anonymous>: no visible global function definition
  for 'formula'
multiCorrMethExprs: no visible global function definition for 'prcomp'
plotFeature: no visible binding for global variable 'lm'
plotRDAMulti: no visible global function definition for 'plot'
plotRDAMulti: no visible global function definition for 'points'
plotRDAMulti: no visible global function definition for 'text'
plotRDAMulti: no visible global function definition for 'legend'
qqplotBand: no visible binding for global variable 'qbeta'
qqplotBand: no visible binding for global variable 'lm'
residualsCorr: no visible global function definition for 'lm'
exportResults,AnalysisResults: no visible global function definition
  for 'write.csv2'
plotRDA,AnalysisRegionResults: no visible global function definition
  for 'plot'
plotRDA,AnalysisRegionResults: no visible global function definition
  for 'text'
plotRDA,AnalysisRegionResults: no visible global function definition
  for 'points'
plotRDA,AnalysisRegionResults: no visible global function definition
  for 'legend'
topRDAhits,AnalysisRegionResults : <anonymous> : <anonymous>: no
  visible global function definition for 'cor.test'
topRDAhits,AnalysisRegionResults : <anonymous>: no visible global
  function definition for 'p.adjust'
Undefined global functions or variables:
  contrasts cor.test formula legend lm model.matrix p.adjust plot
  points prcomp qbeta qt text write.csv2
Consider adding
  importFrom("graphics", "legend", "plot", "points", "text")
  importFrom("stats", "contrasts", "cor.test", "formula", "lm",
             "model.matrix", "p.adjust", "prcomp", "qbeta", "qt")
  importFrom("utils", "write.csv2")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [281s/285s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
plotRegion-methods 66.791  0.891  67.758
plotRDA-methods    66.559  0.934  67.579
topRDAhits-methods 61.284  0.847  62.169
DAPipeline         16.206  0.967  18.308
add.methy-methods   8.576  0.662  11.713
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [71s/71s]
 [71s/72s] 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/MEAL.Rcheck/00check.log’
for details.

* installing *source* package ‘MEAL’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MEAL)

name	user	system	elapsed
AnalysisRegionResults-class	0.002	0.001	0.002
AnalysisResults-class	0.001	0.000	0.001
DAPipeline	16.206	0.967	18.308
DAProbe	0.469	0.014	0.483
DARegion	2.644	0.122	2.772
DARegionAnalysis	3.142	0.162	3.329
MethylationSet-class	0.001	0.001	0.002
RDAset	2.105	0.082	2.189
add.genexp-methods	0.065	0.000	0.065
add.methy-methods	8.576	0.662	11.713
add.set-methods	0.051	0.000	0.051
calculateRelevantSNPs	0.001	0.000	0.000
checkProbes-methods	2.649	0.013	2.664
checkSamples-methods	2.567	0.011	2.580
chrNumToChar	0.001	0.001	0.001
createRanges	0.014	0.000	0.014
explainedVariance	0.030	0.002	0.032
exportResults-methods	2.648	0.093	2.760
filterSet-methods	2.413	0.014	2.431
getGeneVals-methods	2.632	0.044	2.678
getMs-methods	2.338	0.014	2.355
normalSNP	0.001	0.000	0.001
plotBestFeatures	2.866	0.045	2.914
plotEWAS-methods	2.886	0.036	2.925
plotFeature	2.691	0.050	2.744
plotQQ-methods	2.923	0.052	2.977
plotRDA-methods	66.559	0.934	67.579
plotRegion-methods	66.791	0.891	67.758
plotVolcano-methods	3.317	0.174	3.500
prepareMethylationSet	2.507	0.076	2.585
preparePhenotype	0.004	0.000	0.006
topRDAhits-methods	61.284	0.847	62.169