BioC 3.3: CHECK report for MEAL on linux2.bioconductor.org

Package: MEAL

Version: 1.0.1

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings MEAL_1.0.1.tar.gz

StartedAt: 2015-10-27 05:31:14 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:36:57 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 343.2 seconds

RetCode: 0

Status:  OK

CheckDir: MEAL.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-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-3.3-bioc/meat/MEAL.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ... [21s/21s] 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’
Undefined global functions or variables:
  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 ... [75s/75s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
DAPipeline         14.979  0.456  15.453
plotRegion-methods  9.753  0.044   9.801
add.methy-methods   8.799  0.344   9.150
plotRDA-methods     6.349  0.016   6.366
DARegionAnalysis    6.239  0.019   6.267
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [52s/52s]
 [52s/52s] 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-3.3-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	14.979	0.456	15.453
DAProbe	0.314	0.032	0.346
DARegion	1.275	0.081	1.355
DARegionAnalysis	6.239	0.019	6.267
MethylationSet-class	0.001	0.000	0.001
RDAset	1.047	0.024	1.071
add.genexp-methods	0.046	0.000	0.046
add.methy-methods	8.799	0.344	9.150
add.set-methods	0.05	0.00	0.05
calculateRelevantSNPs	0.001	0.000	0.001
checkProbes-methods	0.892	0.000	0.894
checkSamples-methods	0.851	0.004	0.855
chrNumToChar	0.000	0.000	0.001
createRanges	0.013	0.000	0.012
explainedVariance	0.019	0.000	0.020
exportResults-methods	1.110	0.008	1.117
filterSet-methods	0.747	0.012	0.762
getGeneVals-methods	2.894	0.024	2.920
getMs-methods	0.984	0.012	0.996
normalSNP	0.001	0.000	0.001
plotBestFeatures	1.428	0.036	1.465
plotEWAS-methods	1.450	0.044	1.494
plotFeature	0.884	0.004	0.888
plotQQ-methods	1.037	0.004	1.042
plotRDA-methods	6.349	0.016	6.366
plotRegion-methods	9.753	0.044	9.801
plotVolcano-methods	1.475	0.008	1.489
prepareMethylationSet	1.090	0.008	1.101
preparePhenotype	0.000	0.004	0.004