BioC 3.1: CHECK report for PhenStat on petty

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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_2.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-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 ‘2.2.0’
* 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 ... [12s/12s] 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 ... 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 ... [64s/64s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
qqplotRotatedResiduals 8.843  0.181   9.049
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [5s/5s]
 [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: OK

* 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	0.494	0.015	0.510
LRDataset	0.140	0.001	0.141
PhenList-class	0.320	0.003	0.324
PhenList	0.392	0.004	0.396
PhenTestResult-class	2.696	0.225	2.920
PhenTestResult	2.008	0.298	2.306
RRTest	0.137	0.002	0.139
TFDataset	0.768	0.027	0.796
boxplotResidualBatch	1.964	0.323	2.292
boxplotSexGenotype	0.158	0.003	0.162
boxplotSexGenotypeBatch	0.315	0.004	0.320
boxplotSexGenotypeBatchAdjusted	0.174	0.002	0.176
categoricalBarplot	0.365	0.007	0.372
checkDataset	0.102	0.001	0.104
classificationTag	2.239	0.320	2.564
determiningLambda	1.265	0.314	1.581
dim	0.102	0.001	0.103
finalLRModel	0.642	0.006	0.701
finalModel	2.047	0.270	2.319
finalTFModel	1.130	0.024	1.154
htestPhenStat-class	0.293	0.009	0.302
modelFormula	0.001	0.000	0.001
modelFormulaLR	0.001	0.000	0.002
parserOutputSummary	1.839	0.294	2.134
parserOutputSummaryLR	0.631	0.003	0.634
parserOutputTFSummary	0.297	0.002	0.298
plotResidualPredicted	1.963	0.265	2.228
printLROutput	0.667	0.004	0.673
printTabStyle	0.004	0.001	0.004
qqplotGenotype	2.096	0.305	2.404
qqplotRandomEffects	2.226	0.320	2.549
qqplotRotatedResiduals	8.843	0.181	9.049
recommendMethod	0.721	0.003	0.724
reverseTransformValues	0.001	0.000	0.002
scatterplotGenotypeWeight	0.237	0.004	0.242
scatterplotSexGenotypeBatch	0.202	0.004	0.207
startLRModel	0.589	0.009	0.597
startModel	2.977	0.791	3.772
startTFModel	0.929	0.011	0.939
summaryOutput	2.354	0.439	2.797
testDataset	3.593	0.731	4.324
testFinalLRModel	0.451	0.010	0.460
testFinalModel	2.222	0.432	2.658
transformValues	0.001	0.000	0.001
vectorOutput	2.071	0.406	2.479
vectorOutputMatrices	0.301	0.004	0.306

BioC 3.1: CHECK report for PhenStat on petty

Summary

Command output