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: 2017-08-16 00:23:46 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:34:14 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 628.2 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 3.4.1 (2017-06-30)
* 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
topRDAhits-methods 44.208  0.244  44.484
plotRegion-methods 42.168  0.144  42.344
plotRDA-methods    41.168  0.132  41.358
DAPipeline         19.480  3.132  24.303
DARegion            5.748  0.376   6.179
* 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	0.004	0.000	0.003
AnalysisResults-class	0.000	0.000	0.002
DAPipeline	19.480	3.132	24.303
DAProbe	0.904	0.168	1.075
DARegion	5.748	0.376	6.179
DARegionAnalysis	3.168	0.348	3.666
RDAset	1.336	0.184	1.520
calculateRelevantSNPs	0	0	0
createRanges	0.016	0.000	0.019
explainedVariance	0.024	0.000	0.024
exportResults-methods	2.164	0.008	2.173
filterSet-methods	0.840	0.000	0.839
getGeneVals-methods	2.444	0.104	2.550
normalSNP	0.004	0.000	0.001
plotBestFeatures	2.636	0.000	2.639
plotEWAS-methods	2.224	0.008	2.235
plotFeature	1.464	0.060	1.525
plotLM	0.248	0.000	0.249
plotQQ-methods	2.760	0.000	2.757
plotRDA-methods	41.168	0.132	41.358
plotRegion-methods	42.168	0.144	42.344
plotVolcano-methods	2.496	0.004	2.501
prepareMethylationSet	1.184	0.000	1.184
preparePhenotype	0.000	0.000	0.003
topRDAhits-methods	44.208	0.244	44.484