BioC 3.5: CHECK report for MEAL on veracruz2

Package: MEAL

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MEAL_1.6.0.tar.gz

StartedAt: 2017-10-18 05:43:38 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 05:56:48 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 790.7 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_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MEAL.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MEAL/DESCRIPTION’ ... OK
* this is package ‘MEAL’ version ‘1.6.0’
* package encoding: UTF-8
* 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 ... 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
correlationMethSNPs: no visible binding for global variable 'num_cores'
prepareMethylationSet: no visible global function definition for
  'colData'
Undefined global functions or variables:
  colData num_cores
* 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 ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
plotRDA-methods    57.302  1.406  62.155
plotRegion-methods 55.122  1.301  58.071
topRDAhits-methods 53.787  1.791  60.801
DAPipeline         21.365  1.406  23.454
DARegionAnalysis    6.551  0.492   7.257
DARegion            5.972  0.372   6.514
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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-3.5-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	0.003	0.001	0.004
AnalysisResults-class	0.002	0.000	0.003
DAPipeline	21.365	1.406	23.454
DAProbe	0.670	0.068	0.768
DARegion	5.972	0.372	6.514
DARegionAnalysis	6.551	0.492	7.257
RDAset	1.631	0.160	1.844
calculateRelevantSNPs	0.001	0.000	0.000
createRanges	0.025	0.000	0.026
explainedVariance	0.028	0.001	0.032
exportResults-methods	4.066	0.391	4.581
filterSet-methods	0.994	0.026	1.045
getGeneVals-methods	2.914	0.401	3.407
normalSNP	0.001	0.000	0.001
plotBestFeatures	3.573	0.181	3.860
plotEWAS-methods	4.284	0.362	4.779
plotFeature	1.544	0.110	1.720
plotLM	0.331	0.004	0.346
plotQQ-methods	3.444	0.418	3.977
plotRDA-methods	57.302	1.406	62.155
plotRegion-methods	55.122	1.301	58.071
plotVolcano-methods	3.025	0.396	3.510
prepareMethylationSet	1.105	0.131	1.281
preparePhenotype	0.005	0.000	0.006
topRDAhits-methods	53.787	1.791	60.801