BioC 3.4: CHECK report for PhenStat on malbec1

Package: PhenStat

Version: 2.8.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings PhenStat_2.8.0.tar.gz

StartedAt: 2017-04-15 00:24:32 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:26:00 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 88.1 seconds

RetCode: 0

Status:  OK

CheckDir: PhenStat.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings PhenStat_2.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/PhenStat.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘2.8.0’
* 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 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
  ‘/home/biocbuild/bbs-3.4-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	0.248	0.004	0.255
JSONOutput	0.832	0.000	0.835
LRDataset	0.056	0.000	0.058
PhenList-class	0.328	0.004	0.331
PhenList	0.200	0.000	0.198
PhenTestResult-class	0.496	0.000	0.498
PhenTestResult	0.340	0.012	0.353
RRTest	0.080	0.004	0.085
TFDataset	0.292	0.004	0.294
boxplotResidualBatch	0.504	0.000	0.502
boxplotSexGenotype	0.084	0.000	0.084
boxplotSexGenotypeBatch	0.124	0.000	0.124
boxplotSexGenotypeBatchAdjusted	0.072	0.000	0.072
boxplotSexGenotypeResult	0.872	0.004	0.879
boxplotSexGenotypeWeightBatchAdjusted	0.112	0.000	0.116
categoricalBarplot	0.312	0.000	0.313
checkDataset	0.044	0.000	0.044
classificationTag	0.484	0.004	0.490
determiningLambda	0.548	0.060	0.610
dim	0.04	0.00	0.04
finalLRModel	0.352	0.000	0.351
finalModel	0.360	0.000	0.361
finalTFModel	0.608	0.004	0.611
htestPhenStat-class	0.236	0.008	0.245
modelFormula	0.000	0.000	0.001
modelFormulaLR	0.000	0.000	0.001
parserOutputSummary	0.544	0.004	0.551
parserOutputSummaryLR	0.496	0.000	0.496
parserOutputTFSummary	0.076	0.000	0.075
performReverseTransformation	0.004	0.000	0.000
performTransformation	0.000	0.000	0.001
plotResidualPredicted	0.460	0.000	0.463
printLROutput	0.292	0.004	0.299
printTabStyle	0.004	0.000	0.002
qqplotGenotype	0.484	0.000	0.484
qqplotRandomEffects	0.48	0.00	0.48
qqplotRotatedResiduals	3.072	0.004	3.075
recommendMethod	0.248	0.000	0.250
scatterplotGenotypeWeight	0.108	0.000	0.108
scatterplotGenotypeWeightResult	0.832	0.000	0.833
scatterplotSexGenotypeBatch	0.088	0.000	0.087
scatterplotSexGenotypeBatchResult	0.616	0.000	0.615
startLRModel	0.256	0.004	0.261
startModel	0.264	0.000	0.262
startTFModel	0.428	0.004	0.432
summaryOutput	0.572	0.004	0.573
testDataset	0.900	0.000	0.901
testFinalLRModel	0.304	0.000	0.303
testFinalModel	0.604	0.000	0.604
vectorOutput	0.588	0.000	0.588
vectorOutputMatrices	0.132	0.000	0.130