BioC 3.2: CHECK report for MEAL on linux1.bioconductor.org

Package: MEAL

Version: 1.0.1

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MEAL_1.0.1.tar.gz

StartedAt: 2015-10-27 05:23:06 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:29:34 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 388.3 seconds

RetCode: 0

Status:  OK

CheckDir: MEAL.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MEAL_1.0.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/MEAL.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.0.1’
* 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 ... [25s/25s] 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 ... NOTE
Unexported object imported by a ':::' call: ‘S4Vectors:::selectSome’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotVolcano,AnalysisResults: no visible binding for global variable
  ‘adj.p’
* 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 ... [82s/82s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
DAPipeline         15.790  0.568  16.396
plotRegion-methods  8.170  0.048   8.228
add.methy-methods   7.575  0.320   7.904
plotRDA-methods     7.446  0.036   7.512
DARegionAnalysis    6.307  0.052   6.375
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [60s/60s]
 [60s/60s] 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-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	0.000	0.002
DAPipeline	15.790	0.568	16.396
DAProbe	0.540	0.036	0.578
DARegion	2.108	0.024	2.135
DARegionAnalysis	6.307	0.052	6.375
MethylationSet-class	0.001	0.000	0.001
RDAset	0.959	0.040	0.999
add.genexp-methods	0.054	0.000	0.053
add.methy-methods	7.575	0.320	7.904
add.set-methods	0.060	0.000	0.059
calculateRelevantSNPs	0.001	0.000	0.001
checkProbes-methods	1.527	0.024	1.555
checkSamples-methods	1.106	0.032	1.141
chrNumToChar	0.001	0.000	0.001
createRanges	0.020	0.000	0.021
explainedVariance	0.031	0.000	0.032
exportResults-methods	1.781	0.019	1.805
filterSet-methods	1.051	0.004	1.058
getGeneVals-methods	2.741	0.004	2.760
getMs-methods	0.681	0.008	0.690
normalSNP	0.001	0.000	0.000
plotBestFeatures	1.333	0.024	1.359
plotEWAS-methods	1.683	0.080	1.765
plotFeature	1.213	0.004	1.217
plotQQ-methods	1.983	0.012	1.998
plotRDA-methods	7.446	0.036	7.512
plotRegion-methods	8.170	0.048	8.228
plotVolcano-methods	1.840	0.008	1.850
prepareMethylationSet	1.143	0.008	1.154
preparePhenotype	0.004	0.000	0.004