BioC 3.6: CHECK report for PhenStat on veracruz1

Package: PhenStat

Version: 2.11.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PhenStat_2.11.0.tar.gz

StartedAt: 2017-08-16 06:44:57 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 06:46:48 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 111.1 seconds

RetCode: 0

Status:  OK

CheckDir: PhenStat.Rcheck

Warnings: 0

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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_2.11.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/PhenStat.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.11.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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-3.6-bioc/meat/PhenStat.Rcheck/00check.log’
for details.

* installing *source* package ‘PhenStat’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PhenStat)

name	user	system	elapsed
FisherExactTest	0.434	0.020	0.475
JSONOutput	2.087	0.021	2.169
LRDataset	0.094	0.001	0.096
PhenList-class	0.250	0.004	0.254
PhenList	0.423	0.005	0.442
PhenTestResult-class	1.150	0.022	1.208
PhenTestResult	0.398	0.003	0.409
RRTest	0.141	0.001	0.147
TFDataset	0.309	0.002	0.324
boxplotResidualBatch	0.497	0.004	0.507
boxplotSexGenotype	0.077	0.001	0.080
boxplotSexGenotypeBatch	0.144	0.007	0.158
boxplotSexGenotypeBatchAdjusted	0.061	0.002	0.064
boxplotSexGenotypeResult	0.587	0.008	0.602
boxplotSexGenotypeWeightBatchAdjusted	0.079	0.001	0.081
categoricalBarplot	0.196	0.002	0.202
checkDataset	0.056	0.001	0.057
classificationTag	0.565	0.004	0.578
determiningLambda	0.647	0.137	0.800
dim	0.043	0.001	0.047
finalLRModel	0.532	0.004	0.542
finalModel	0.377	0.008	0.390
finalTFModel	0.612	0.007	0.624
htestPhenStat-class	0.204	0.005	0.210
modelFormula	0.001	0.000	0.001
modelFormulaLR	0.001	0.000	0.001
parserOutputSummary	0.538	0.006	0.568
parserOutputSummaryLR	0.444	0.006	0.460
parserOutputTFSummary	0.382	0.002	0.403
performReverseTransformation	0.001	0.000	0.000
performTransformation	0.000	0.000	0.001
plotResidualPredicted	0.592	0.007	0.614
printLROutput	0.396	0.006	0.407
printTabStyle	0.001	0.000	0.002
qqplotGenotype	0.581	0.003	0.605
qqplotRandomEffects	0.562	0.008	0.599
qqplotRotatedResiduals	4.180	0.024	4.276
recommendMethod	0.336	0.003	0.342
scatterplotGenotypeWeight	0.130	0.002	0.141
scatterplotGenotypeWeightResult	0.708	0.007	0.740
scatterplotSexGenotypeBatch	0.104	0.002	0.110
scatterplotSexGenotypeBatchResult	0.680	0.003	0.712
startLRModel	0.282	0.003	0.294
startModel	0.240	0.001	0.245
startTFModel	0.457	0.003	0.465
summaryOutput	0.824	0.012	0.847
testDataset	1.030	0.018	1.070
testFinalLRModel	0.320	0.003	0.333
testFinalModel	0.819	0.005	0.842
vectorOutput	0.974	0.023	1.012
vectorOutputMatrices	0.257	0.009	0.271