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: 2017-08-16 06:27:55 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 06:29:48 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 113.7 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 3.4.1 (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 ‘2.10.0’
* 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	0.457	0.019	0.493
JSONOutput	2.091	0.027	2.193
LRDataset	0.079	0.002	0.080
PhenList-class	0.251	0.005	0.265
PhenList	0.425	0.005	0.440
PhenTestResult-class	1.229	0.019	1.281
PhenTestResult	0.493	0.006	0.515
RRTest	0.210	0.001	0.220
TFDataset	0.410	0.004	0.417
boxplotResidualBatch	0.635	0.008	0.660
boxplotSexGenotype	0.103	0.002	0.109
boxplotSexGenotypeBatch	0.199	0.009	0.217
boxplotSexGenotypeBatchAdjusted	0.097	0.001	0.100
boxplotSexGenotypeResult	0.749	0.006	0.773
boxplotSexGenotypeWeightBatchAdjusted	0.106	0.001	0.109
categoricalBarplot	0.234	0.002	0.239
checkDataset	0.062	0.001	0.071
classificationTag	0.591	0.004	0.609
determiningLambda	0.776	0.165	0.958
dim	0.059	0.001	0.063
finalLRModel	0.694	0.007	0.719
finalModel	0.470	0.007	0.484
finalTFModel	0.746	0.003	0.769
htestPhenStat-class	0.242	0.004	0.254
modelFormula	0.001	0.000	0.001
modelFormulaLR	0.001	0.000	0.001
parserOutputSummary	0.591	0.003	0.619
parserOutputSummaryLR	0.475	0.008	0.499
parserOutputTFSummary	0.351	0.002	0.355
performReverseTransformation	0.001	0.001	0.000
performTransformation	0.001	0.000	0.000
plotResidualPredicted	0.507	0.006	0.526
printLROutput	0.319	0.007	0.342
printTabStyle	0.002	0.001	0.002
qqplotGenotype	0.542	0.002	0.556
qqplotRandomEffects	0.528	0.006	0.548
qqplotRotatedResiduals	3.753	0.021	3.875
recommendMethod	0.361	0.002	0.374
scatterplotGenotypeWeight	0.135	0.004	0.147
scatterplotGenotypeWeightResult	0.812	0.008	0.843
scatterplotSexGenotypeBatch	0.109	0.002	0.114
scatterplotSexGenotypeBatchResult	0.706	0.005	0.732
startLRModel	0.321	0.004	0.333
startModel	0.324	0.003	0.327
startTFModel	0.585	0.003	0.595
summaryOutput	0.842	0.006	0.866
testDataset	1.233	0.012	1.287
testFinalLRModel	0.363	0.008	0.377
testFinalModel	0.911	0.006	0.936
vectorOutput	1.024	0.015	1.066
vectorOutputMatrices	0.240	0.001	0.248