BioC 3.2: CHECK report for PhenStat on perceval

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PhenStat_2.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/PhenStat.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PhenStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PhenStat’ version ‘2.3.0’
* 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 ‘PhenStat’ can be installed ... [9s/9s] OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   3.0Mb
* 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [54s/54s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
qqplotRotatedResiduals 8.347  0.243   8.612
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [4s/4s]
 [5s/5s] 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/PhenStat.Rcheck/00check.log’
for details.

* installing *source* package ‘PhenStat’ ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
* DONE (PhenStat)

name	user	system	elapsed
FisherExactTest	0.548	0.020	0.567
LRDataset	0.104	0.002	0.106
PhenList-class	0.244	0.004	0.248
PhenList	0.263	0.004	0.266
PhenTestResult-class	2.267	0.285	2.553
PhenTestResult	1.697	0.361	2.058
RRTest	0.121	0.004	0.125
TFDataset	0.497	0.052	0.549
boxplotResidualBatch	1.433	0.363	1.797
boxplotSexGenotype	0.106	0.004	0.110
boxplotSexGenotypeBatch	0.200	0.004	0.204
boxplotSexGenotypeBatchAdjusted	0.100	0.002	0.103
categoricalBarplot	0.544	0.004	0.548
checkDataset	0.056	0.001	0.056
classificationTag	1.402	0.363	1.769
determiningLambda	0.916	0.355	1.273
dim	0.058	0.001	0.059
finalLRModel	0.463	0.005	0.509
finalModel	1.686	0.342	2.034
finalTFModel	0.973	0.014	0.990
htestPhenStat-class	0.253	0.004	0.257
modelFormula	0.001	0.000	0.001
modelFormulaLR	0.001	0.000	0.001
parserOutputSummary	1.506	0.372	1.886
parserOutputSummaryLR	0.746	0.006	0.755
parserOutputTFSummary	0.248	0.002	0.251
plotResidualPredicted	1.422	0.360	1.817
printLROutput	0.720	0.005	0.726
printTabStyle	0.002	0.000	0.003
qqplotGenotype	1.443	0.363	1.811
qqplotRandomEffects	1.719	0.352	2.091
qqplotRotatedResiduals	8.347	0.243	8.612
recommendMethod	0.504	0.005	0.510
reverseTransformValues	0.000	0.000	0.001
scatterplotGenotypeWeight	0.163	0.006	0.170
scatterplotSexGenotypeBatch	0.116	0.004	0.121
startLRModel	0.385	0.014	0.400
startModel	2.117	0.853	2.972
startTFModel	0.860	0.010	0.871
summaryOutput	1.684	0.442	2.126
testDataset	3.202	0.908	4.114
testFinalLRModel	0.411	0.008	0.419
testFinalModel	1.488	0.458	1.947
transformValues	0	0	0
vectorOutput	1.516	0.454	1.970
vectorOutputMatrices	0.232	0.018	0.250

BioC 3.2: CHECK report for PhenStat on perceval

Summary

Command output