BioC 3.4: CHECK report for MEAL on morelia

Package: MEAL

Version: 1.4.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MEAL_1.4.2.tar.gz

StartedAt: 2017-04-15 04:37:25 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 04:50:05 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 759.8 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_1.4.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/MEAL.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.4.2’
* 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
plotRDA-methods    53.061  1.048  54.481
plotRegion-methods 52.227  1.084  53.350
topRDAhits-methods 50.950  1.141  52.129
DAPipeline         15.481  0.906  17.699
DARegionAnalysis    4.725  0.320   5.093
* 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-3.4-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	0.003
AnalysisResults-class	0.001	0.000	0.001
DAPipeline	15.481	0.906	17.699
DAProbe	0.884	0.041	0.925
DARegion	4.240	0.257	4.498
DARegionAnalysis	4.725	0.320	5.093
RDAset	3.813	0.255	4.068
calculateRelevantSNPs	0.000	0.000	0.001
createRanges	0.017	0.000	0.017
explainedVariance	0.023	0.001	0.024
exportResults-methods	3.765	0.211	3.979
filterSet-methods	2.150	0.021	2.172
getGeneVals-methods	4.058	0.212	4.273
normalSNP	0.001	0.000	0.001
plotBestFeatures	4.165	0.144	4.314
plotEWAS-methods	4.613	0.197	4.816
plotFeature	2.549	0.100	2.651
plotLM	0.188	0.002	0.190
plotQQ-methods	4.727	0.205	4.941
plotRDA-methods	53.061	1.048	54.481
plotRegion-methods	52.227	1.084	53.350
plotVolcano-methods	4.264	0.277	4.543
preparePhenotype	0.006	0.000	0.007
topRDAhits-methods	50.950	1.141	52.129