BioC 3.2: CHECK report for MEAL on oaxaca

Package: MEAL

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MEAL_1.0.1.tar.gz

StartedAt: 2015-10-27 05:20:40 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:28:39 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 478.9 seconds

RetCode: 0

Status:  OK

CheckDir: MEAL.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MEAL_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/MEAL.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.0.1’
* 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 ... [29s/30s] 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 ... [104s/109s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
DAPipeline         14.905  1.014  18.140
plotRegion-methods 12.142  0.727  12.878
plotRDA-methods    10.521  0.672  11.213
add.methy-methods   8.352  0.809  12.414
DARegionAnalysis    7.700  0.336   8.056
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [74s/75s]
 [75s/75s] 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/MEAL.Rcheck/00check.log’
for details.

* installing *source* package ‘MEAL’ ...
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
* DONE (MEAL)

name	user	system	elapsed
AnalysisRegionResults-class	0.003	0.001	0.005
AnalysisResults-class	0.002	0.000	0.003
DAPipeline	14.905	1.014	18.140
DAProbe	0.602	0.036	0.639
DARegion	2.630	0.128	2.759
DARegionAnalysis	7.700	0.336	8.056
MethylationSet-class	0.001	0.000	0.001
RDAset	1.819	0.089	1.910
add.genexp-methods	0.078	0.000	0.079
add.methy-methods	8.352	0.809	12.414
add.set-methods	0.048	0.000	0.049
calculateRelevantSNPs	0.001	0.000	0.000
checkProbes-methods	1.801	0.036	1.838
checkSamples-methods	1.630	0.032	1.665
chrNumToChar	0.001	0.000	0.001
createRanges	0.02	0.00	0.02
explainedVariance	0.037	0.002	0.039
exportResults-methods	2.404	0.144	2.567
filterSet-methods	1.638	0.035	1.683
getGeneVals-methods	3.333	0.195	3.532
getMs-methods	1.417	0.033	1.449
normalSNP	0.001	0.000	0.001
plotBestFeatures	2.061	0.124	2.187
plotEWAS-methods	2.398	0.204	2.603
plotFeature	2.145	0.045	2.197
plotQQ-methods	2.676	0.243	2.919
plotRDA-methods	10.521	0.672	11.213
plotRegion-methods	12.142	0.727	12.878
plotVolcano-methods	2.664	0.203	2.869
prepareMethylationSet	1.875	0.089	1.964
preparePhenotype	0.006	0.001	0.007