BioC 3.2: CHECK report for PhenStat on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings PhenStat_2.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-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 ‘2.3.0’
* 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 ... [6s/6s] 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 ... [38s/38s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
qqplotRotatedResiduals 7.49   0.02   7.509
* 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: 1 NOTE
See
  ‘/home/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	0.332	0.000	0.332
LRDataset	0.077	0.000	0.077
PhenList-class	0.214	0.000	0.214
PhenList	0.183	0.008	0.191
PhenTestResult-class	1.692	0.028	1.719
PhenTestResult	1.337	0.048	1.396
RRTest	0.086	0.004	0.089
TFDataset	0.330	0.020	0.351
boxplotResidualBatch	1.292	0.008	1.299
boxplotSexGenotype	0.079	0.004	0.083
boxplotSexGenotypeBatch	0.147	0.000	0.147
boxplotSexGenotypeBatchAdjusted	0.076	0.000	0.077
categoricalBarplot	0.164	0.000	0.163
checkDataset	0.046	0.000	0.047
classificationTag	1.344	0.016	1.360
determiningLambda	0.733	0.040	0.783
dim	0.045	0.000	0.045
finalLRModel	0.322	0.004	0.325
finalModel	1.253	0.064	1.317
finalTFModel	0.791	0.004	0.794
htestPhenStat-class	0.158	0.004	0.162
modelFormula	0.001	0.000	0.000
modelFormulaLR	0.000	0.000	0.001
parserOutputSummary	1.239	0.016	1.253
parserOutputSummaryLR	0.327	0.000	0.329
parserOutputTFSummary	0.177	0.004	0.201
plotResidualPredicted	1.375	0.008	1.402
printLROutput	0.441	0.000	0.441
printTabStyle	0.002	0.000	0.001
qqplotGenotype	1.198	0.000	1.197
qqplotRandomEffects	1.288	0.000	1.287
qqplotRotatedResiduals	7.490	0.020	7.509
recommendMethod	0.316	0.004	0.320
reverseTransformValues	0.000	0.000	0.001
scatterplotGenotypeWeight	0.113	0.000	0.115
scatterplotSexGenotypeBatch	0.093	0.000	0.094
startLRModel	0.319	0.004	0.320
startModel	1.714	0.000	1.717
startTFModel	0.595	0.000	0.608
summaryOutput	1.573	0.008	1.580
testDataset	2.516	0.144	2.658
testFinalLRModel	0.324	0.000	0.327
testFinalModel	1.483	0.004	1.487
transformValues	0	0	0
vectorOutput	1.385	0.004	1.395
vectorOutputMatrices	0.182	0.008	0.190

BioC 3.2: CHECK report for PhenStat on zin1

Summary

Command output