BioC 3.1: CHECK report for PhenStat on zin2

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings PhenStat_2.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/PhenStat.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 ‘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 ... [6s/6s] 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 ... [38s/38s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
qqplotRotatedResiduals 7.299  0.141   7.433
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [3s/3s]
 [3s/3s] 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	0.337	0.000	0.337
LRDataset	0.066	0.000	0.066
PhenList-class	0.193	0.000	0.193
PhenList	0.193	0.000	0.193
PhenTestResult-class	1.702	0.028	1.728
PhenTestResult	1.370	0.020	1.389
RRTest	0.091	0.000	0.091
TFDataset	0.348	0.012	0.359
boxplotResidualBatch	1.241	0.008	1.259
boxplotSexGenotype	0.08	0.00	0.08
boxplotSexGenotypeBatch	0.158	0.000	0.158
boxplotSexGenotypeBatchAdjusted	0.076	0.000	0.076
categoricalBarplot	0.169	0.000	0.169
checkDataset	0.044	0.000	0.047
classificationTag	1.413	0.012	1.426
determiningLambda	0.733	0.040	0.772
dim	0.041	0.000	0.041
finalLRModel	0.315	0.000	0.318
finalModel	1.395	0.023	1.422
finalTFModel	0.650	0.000	0.656
htestPhenStat-class	0.164	0.000	0.164
modelFormula	0.000	0.000	0.001
modelFormulaLR	0.001	0.000	0.001
parserOutputSummary	1.348	0.023	1.392
parserOutputSummaryLR	0.319	0.000	0.319
parserOutputTFSummary	0.164	0.000	0.164
plotResidualPredicted	1.466	0.020	1.485
printLROutput	0.357	0.000	0.357
printTabStyle	0.001	0.000	0.001
qqplotGenotype	1.264	0.028	1.293
qqplotRandomEffects	1.374	0.040	1.413
qqplotRotatedResiduals	7.299	0.141	7.433
recommendMethod	0.448	0.000	0.449
reverseTransformValues	0.000	0.000	0.001
scatterplotGenotypeWeight	0.124	0.000	0.124
scatterplotSexGenotypeBatch	0.102	0.000	0.102
startLRModel	0.314	0.007	0.322
startModel	1.718	0.008	1.728
startTFModel	0.636	0.003	0.637
summaryOutput	1.427	0.068	1.502
testDataset	2.610	0.104	2.722
testFinalLRModel	0.303	0.004	0.307
testFinalModel	1.481	0.016	1.497
transformValues	0	0	0
vectorOutput	1.365	0.032	1.395
vectorOutputMatrices	0.158	0.000	0.159

BioC 3.1: CHECK report for PhenStat on zin2

Summary

Command output