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: 2017-08-16 04:57:18 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 05:09:58 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 760.2 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 3.4.1 (2017-06-30)
* 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     59.357  0.950  62.729
topRDAhits-methods  53.842  1.452  57.256
plotRegion-methods  53.260  0.989  55.795
DAPipeline          20.876  1.181  22.722
DARegion             5.184  0.308   5.637
plotEWAS-methods     4.946  0.225   5.319
DARegionAnalysis     4.708  0.379   5.200
getGeneVals-methods  4.651  0.267   5.092
* 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	0.000	0.003
AnalysisResults-class	0.002	0.001	0.002
DAPipeline	20.876	1.181	22.722
DAProbe	1.011	0.127	1.182
DARegion	5.184	0.308	5.637
DARegionAnalysis	4.708	0.379	5.200
RDAset	1.653	0.124	1.834
calculateRelevantSNPs	0	0	0
createRanges	0.023	0.001	0.023
explainedVariance	0.030	0.002	0.032
exportResults-methods	3.574	0.250	3.939
filterSet-methods	1.183	0.023	1.240
getGeneVals-methods	4.651	0.267	5.092
normalSNP	0.001	0.001	0.001
plotBestFeatures	3.725	0.131	3.954
plotEWAS-methods	4.946	0.225	5.319
plotFeature	2.025	0.188	2.461
plotLM	0.348	0.002	0.384
plotQQ-methods	4.233	0.301	4.994
plotRDA-methods	59.357	0.950	62.729
plotRegion-methods	53.260	0.989	55.795
plotVolcano-methods	3.668	0.329	4.095
prepareMethylationSet	1.315	0.128	1.485
preparePhenotype	0.004	0.001	0.005
topRDAhits-methods	53.842	1.452	57.256