BioC 3.5: CHECK report for MEAL on oaxaca

Package: MEAL

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MEAL_1.5.0.tar.gz

StartedAt: 2016-11-20 03:21:16 -0800 (Sun, 20 Nov 2016)

EndedAt: 2016-11-20 03:32:31 -0800 (Sun, 20 Nov 2016)

EllapsedTime: 675.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MEAL.Rcheck

Warnings: 1

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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_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MEAL.Rcheck’
* using R Under development (unstable) (2016-10-21 r71549)
* 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 ‘1.5.0’
* 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'multiCorrMethExprs'
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
plotRegion-methods 61.085  0.916  62.053
plotRDA-methods    56.371  0.889  57.290
topRDAhits-methods 54.811  0.943  55.788
DAPipeline         16.484  0.878  17.890
DARegionAnalysis    4.896  0.210   5.227
* 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 WARNING
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	0.002
AnalysisResults-class	0.001	0.000	0.001
DAPipeline	16.484	0.878	17.890
DAProbe	0.982	0.039	1.023
DARegion	4.014	0.119	4.137
DARegionAnalysis	4.896	0.210	5.227
RDAset	3.385	0.081	3.468
calculateRelevantSNPs	0.001	0.000	0.001
createRanges	0.015	0.000	0.016
explainedVariance	0.031	0.002	0.032
exportResults-methods	3.250	0.055	3.306
filterSet-methods	2.411	0.045	2.456
getGeneVals-methods	3.302	0.098	3.401
normalSNP	0.001	0.000	0.001
plotBestFeatures	3.279	0.052	3.332
plotEWAS-methods	3.832	0.050	3.884
plotFeature	3.168	0.058	3.238
plotLM	0.250	0.006	0.261
plotQQ-methods	3.827	0.067	3.896
plotRDA-methods	56.371	0.889	57.290
plotRegion-methods	61.085	0.916	62.053
plotVolcano-methods	3.994	0.212	4.209
preparePhenotype	0.003	0.000	0.004
topRDAhits-methods	54.811	0.943	55.788