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_2.4.0.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 (2015-10-08 r69496)
* 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 ‘2.4.0’
* 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 ... [8s/9s] OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   2.9Mb
* 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 ... [32s/32s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [3s/3s]
 [4s/4s] 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	0.459	0.011	0.470
JSONOutput	1.175	0.009	1.183
LRDataset	0.277	0.001	0.277
PhenList-class	0.299	0.009	0.306
PhenList	0.302	0.002	0.304
PhenTestResult-class	0.784	0.005	0.789
PhenTestResult	0.554	0.001	0.555
RRTest	0.129	0.001	0.131
TFDataset	0.503	0.028	0.531
boxplotResidualBatch	0.726	0.007	0.734
boxplotSexGenotype	0.116	0.002	0.119
boxplotSexGenotypeBatch	0.220	0.003	0.224
boxplotSexGenotypeBatchAdjusted	0.108	0.001	0.110
boxplotSexGenotypeResult	1.076	0.003	1.080
boxplotSexGenotypeWeightBatchAdjusted	0.102	0.001	0.104
categoricalBarplot	0.231	0.002	0.233
checkDataset	0.063	0.001	0.063
classificationTag	0.725	0.002	0.727
determiningLambda	0.858	0.238	1.096
dim	0.065	0.001	0.065
finalLRModel	0.440	0.004	0.473
finalModel	0.550	0.007	0.557
finalTFModel	0.793	0.009	0.801
htestPhenStat-class	0.249	0.006	0.255
modelFormula	0.001	0.000	0.001
modelFormulaLR	0.001	0.000	0.001
parserOutputSummary	0.716	0.003	0.718
parserOutputSummaryLR	0.626	0.004	0.630
parserOutputTFSummary	0.117	0.001	0.118
performReverseTransformation	0.001	0.000	0.000
performTransformation	0.001	0.000	0.001
plotResidualPredicted	0.715	0.003	0.718
printLROutput	0.432	0.002	0.434
printTabStyle	0.002	0.000	0.002
qqplotGenotype	0.723	0.003	0.727
qqplotRandomEffects	0.713	0.002	0.715
qqplotRotatedResiduals	4.207	0.042	4.249
recommendMethod	0.455	0.004	0.460
scatterplotGenotypeWeight	0.170	0.003	0.174
scatterplotGenotypeWeightResult	0.959	0.008	0.967
scatterplotSexGenotypeBatch	0.138	0.003	0.143
scatterplotSexGenotypeBatchResult	0.948	0.009	0.958
startLRModel	0.402	0.003	0.405
startModel	0.608	0.007	0.615
startTFModel	0.708	0.004	0.712
summaryOutput	0.955	0.009	0.963
testDataset	1.457	0.016	1.473
testFinalLRModel	0.442	0.002	0.444
testFinalModel	0.917	0.008	0.925
vectorOutput	0.951	0.008	0.958
vectorOutputMatrices	0.237	0.002	0.240

BioC 3.2: CHECK report for PhenStat on perceval

Summary

Command output