BioC 3.6: CHECK report for PhenStat on malbec1

Package: PhenStat

Version: 2.11.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings PhenStat_2.11.0.tar.gz

StartedAt: 2017-08-16 01:22:28 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:23:57 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 89.5 seconds

RetCode: 0

Status:  OK

CheckDir: PhenStat.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings PhenStat_2.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/PhenStat.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘2.11.0’
* 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 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-3.6-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	0.352	0.004	0.355
JSONOutput	1.708	0.020	1.728
LRDataset	0.056	0.000	0.058
PhenList-class	0.188	0.004	0.191
PhenList	0.200	0.000	0.197
PhenTestResult-class	0.956	0.000	0.957
PhenTestResult	0.356	0.008	0.362
RRTest	0.168	0.000	0.168
TFDataset	0.284	0.000	0.286
boxplotResidualBatch	0.576	0.016	0.593
boxplotSexGenotype	0.248	0.004	0.253
boxplotSexGenotypeBatch	0.132	0.000	0.129
boxplotSexGenotypeBatchAdjusted	0.068	0.000	0.067
boxplotSexGenotypeResult	0.784	0.000	0.785
boxplotSexGenotypeWeightBatchAdjusted	0.068	0.000	0.066
categoricalBarplot	0.136	0.000	0.137
checkDataset	0.044	0.000	0.043
classificationTag	0.468	0.004	0.475
determiningLambda	0.524	0.016	0.539
dim	0.04	0.00	0.04
finalLRModel	0.552	0.000	0.554
finalModel	0.380	0.000	0.381
finalTFModel	0.584	0.000	0.587
htestPhenStat-class	0.124	0.008	0.132
modelFormula	0	0	0
modelFormulaLR	0	0	0
parserOutputSummary	0.484	0.000	0.484
parserOutputSummaryLR	0.420	0.000	0.422
parserOutputTFSummary	0.336	0.000	0.337
performReverseTransformation	0	0	0
performTransformation	0	0	0
plotResidualPredicted	0.464	0.004	0.467
printLROutput	0.496	0.000	0.498
printTabStyle	0.000	0.000	0.002
qqplotGenotype	0.456	0.008	0.465
qqplotRandomEffects	0.456	0.004	0.457
qqplotRotatedResiduals	2.952	0.016	2.971
recommendMethod	0.38	0.00	0.38
scatterplotGenotypeWeight	0.284	0.000	0.287
scatterplotGenotypeWeightResult	0.656	0.012	0.667
scatterplotSexGenotypeBatch	0.080	0.000	0.077
scatterplotSexGenotypeBatchResult	0.596	0.000	0.599
startLRModel	0.252	0.000	0.256
startModel	0.288	0.004	0.294
startTFModel	0.452	0.000	0.450
summaryOutput	0.64	0.00	0.64
testDataset	0.896	0.008	0.905
testFinalLRModel	0.304	0.004	0.308
testFinalModel	0.576	0.012	0.588
vectorOutput	0.732	0.000	0.729
vectorOutputMatrices	0.168	0.000	0.169