BioC 3.5: CHECK report for PhenStat on veracruz2

Package: PhenStat

Version: 2.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PhenStat_2.10.0.tar.gz

StartedAt: 2017-10-18 07:15:24 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 07:17:21 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 116.4 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_2.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/PhenStat.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘2.10.0’
* 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-3.5-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	0.314	0.009	0.331
JSONOutput	2.283	0.036	2.389
LRDataset	0.109	0.003	0.118
PhenList-class	0.268	0.006	0.279
PhenList	0.258	0.003	0.270
PhenTestResult-class	1.336	0.025	1.399
PhenTestResult	0.487	0.006	0.511
RRTest	0.222	0.009	0.236
TFDataset	0.423	0.018	0.448
boxplotResidualBatch	0.640	0.009	0.670
boxplotSexGenotype	0.112	0.002	0.131
boxplotSexGenotypeBatch	0.188	0.003	0.196
boxplotSexGenotypeBatchAdjusted	0.099	0.002	0.113
boxplotSexGenotypeResult	0.819	0.011	0.858
boxplotSexGenotypeWeightBatchAdjusted	0.099	0.002	0.105
categoricalBarplot	0.247	0.003	0.256
checkDataset	0.065	0.001	0.067
classificationTag	0.783	0.005	0.807
determiningLambda	0.612	0.179	0.808
dim	0.061	0.001	0.062
finalLRModel	0.711	0.006	0.740
finalModel	0.459	0.007	0.481
finalTFModel	0.774	0.009	0.803
htestPhenStat-class	0.236	0.004	0.247
modelFormula	0.001	0.000	0.001
modelFormulaLR	0.000	0.000	0.001
parserOutputSummary	0.605	0.006	0.639
parserOutputSummaryLR	0.530	0.007	0.571
parserOutputTFSummary	0.462	0.003	0.473
performReverseTransformation	0.001	0.001	0.001
performTransformation	0.001	0.000	0.001
plotResidualPredicted	0.587	0.004	0.615
printLROutput	0.396	0.004	0.411
printTabStyle	0.001	0.000	0.002
qqplotGenotype	0.628	0.004	0.648
qqplotRandomEffects	0.787	0.009	0.814
qqplotRotatedResiduals	3.633	0.042	3.787
recommendMethod	0.298	0.003	0.310
scatterplotGenotypeWeight	0.278	0.007	0.294
scatterplotGenotypeWeightResult	0.631	0.011	0.656
scatterplotSexGenotypeBatch	0.090	0.003	0.095
scatterplotSexGenotypeBatchResult	0.691	0.011	0.716
startLRModel	0.331	0.004	0.344
startModel	0.353	0.011	0.384
startTFModel	0.626	0.009	0.661
summaryOutput	0.766	0.014	0.811
testDataset	1.178	0.014	1.223
testFinalLRModel	0.385	0.005	0.410
testFinalModel	0.783	0.010	0.808
vectorOutput	0.977	0.008	1.020
vectorOutputMatrices	0.286	0.005	0.312