BioC 3.5: CHECK report for MEAL on toluca2

Package: MEAL

Version: 1.5.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MEAL_1.5.4.tar.gz

StartedAt: 2017-04-23 06:16:30 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 06:30:47 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 857.6 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_1.5.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MEAL.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.5.4’
* 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    67.976  1.145  73.134
plotRegion-methods 64.914  1.158  66.645
topRDAhits-methods 64.601  1.231  66.215
DAPipeline         21.270  1.297  22.814
plotBestFeatures    5.625  0.169   5.892
DARegion            5.309  0.345   5.746
DARegionAnalysis    4.557  0.447   5.033
* 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	0.002	0.001	0.002
AnalysisResults-class	0.002	0.000	0.002
DAPipeline	21.270	1.297	22.814
DAProbe	1.025	0.137	1.168
DARegion	5.309	0.345	5.746
DARegionAnalysis	4.557	0.447	5.033
RDAset	1.460	0.124	1.609
calculateRelevantSNPs	0.001	0.001	0.001
createRanges	0.313	0.017	0.340
explainedVariance	0.026	0.001	0.027
exportResults-methods	3.223	0.258	3.523
filterSet-methods	1.054	0.026	1.093
getGeneVals-methods	2.833	0.257	3.099
normalSNP	0.001	0.000	0.001
plotBestFeatures	5.625	0.169	5.892
plotEWAS-methods	3.511	0.258	3.812
plotFeature	2.930	0.209	3.169
plotLM	0.394	0.002	0.400
plotQQ-methods	3.075	0.253	3.640
plotRDA-methods	67.976	1.145	73.134
plotRegion-methods	64.914	1.158	66.645
plotVolcano-methods	3.127	0.340	3.607
prepareMethylationSet	1.083	0.137	1.230
preparePhenotype	0.006	0.001	0.006
topRDAhits-methods	64.601	1.231	66.215