BioC 3.5: CHECK report for MEAL on malbec2

Package: MEAL

Version: 1.6.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings MEAL_1.6.0.tar.gz

StartedAt: 2017-10-18 00:35:40 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:45:44 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 603.8 seconds

RetCode: 0

Status:  OK

CheckDir: MEAL.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings MEAL_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/MEAL.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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    42.548  0.112  42.680
topRDAhits-methods 40.112  0.292  40.432
plotRegion-methods 39.928  0.404  40.351
DAPipeline         18.188  1.012  19.992
* 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
  ‘/home/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	0.024	0.000	0.027
AnalysisResults-class	0.000	0.000	0.001
DAPipeline	18.188	1.012	19.992
DAProbe	2.124	0.004	2.129
DARegion	4.340	0.252	4.619
DARegionAnalysis	3.880	0.088	4.011
RDAset	1.120	0.008	1.125
calculateRelevantSNPs	0	0	0
createRanges	0.020	0.000	0.018
explainedVariance	0.024	0.000	0.023
exportResults-methods	3.908	0.076	3.984
filterSet-methods	0.836	0.028	0.864
getGeneVals-methods	3.448	0.164	3.611
normalSNP	0.000	0.000	0.001
plotBestFeatures	2.684	0.172	2.856
plotEWAS-methods	2.724	0.160	2.886
plotFeature	1.22	0.08	1.30
plotLM	0.244	0.000	0.242
plotQQ-methods	2.828	0.136	2.965
plotRDA-methods	42.548	0.112	42.680
plotRegion-methods	39.928	0.404	40.351
plotVolcano-methods	2.360	0.352	2.715
prepareMethylationSet	0.904	0.000	0.906
preparePhenotype	0.004	0.000	0.004
topRDAhits-methods	40.112	0.292	40.432