BioC 3.4: CHECK report for PhenStat on morelia

Package: PhenStat

Version: 2.7.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PhenStat_2.7.1.tar.gz

StartedAt: 2016-09-20 11:11:36 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 11:13:04 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 88.3 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_2.7.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/PhenStat.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.7.1’
* 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
Examples with CPU or elapsed time > 5s
                        user system elapsed
qqplotRotatedResiduals 5.079   0.04   5.124
* 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-3.4-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	0.368	0.006	0.375
JSONOutput	1.089	0.007	1.096
LRDataset	0.085	0.001	0.086
PhenList-class	0.254	0.002	0.256
PhenList	0.247	0.002	0.249
PhenTestResult-class	0.698	0.004	0.702
PhenTestResult	0.444	0.007	0.450
RRTest	0.094	0.001	0.094
TFDataset	0.438	0.014	0.563
boxplotResidualBatch	0.579	0.005	0.584
boxplotSexGenotype	0.097	0.003	0.112
boxplotSexGenotypeBatch	0.142	0.003	0.145
boxplotSexGenotypeBatchAdjusted	0.083	0.002	0.085
boxplotSexGenotypeResult	0.852	0.013	0.868
boxplotSexGenotypeWeightBatchAdjusted	0.075	0.002	0.078
categoricalBarplot	0.190	0.002	0.192
checkDataset	0.049	0.001	0.049
classificationTag	0.615	0.005	0.622
determiningLambda	0.702	0.125	0.827
dim	0.052	0.001	0.053
finalLRModel	0.353	0.005	0.422
finalModel	0.606	0.009	0.615
finalTFModel	0.536	0.009	0.545
htestPhenStat-class	0.181	0.003	0.183
modelFormula	0.001	0.000	0.001
modelFormulaLR	0.000	0.000	0.001
parserOutputSummary	0.611	0.004	0.616
parserOutputSummaryLR	0.482	0.004	0.486
parserOutputTFSummary	0.104	0.001	0.106
performReverseTransformation	0.000	0.000	0.001
performTransformation	0.000	0.000	0.001
plotResidualPredicted	0.539	0.002	0.540
printLROutput	0.354	0.001	0.355
printTabStyle	0.001	0.000	0.001
qqplotGenotype	0.627	0.002	0.630
qqplotRandomEffects	0.821	0.004	0.846
qqplotRotatedResiduals	5.079	0.040	5.124
recommendMethod	0.294	0.004	0.298
scatterplotGenotypeWeight	0.118	0.002	0.121
scatterplotGenotypeWeightResult	0.691	0.009	0.702
scatterplotSexGenotypeBatch	0.099	0.002	0.100
scatterplotSexGenotypeBatchResult	0.676	0.007	0.684
startLRModel	0.269	0.001	0.270
startModel	0.254	0.003	0.258
startTFModel	0.465	0.006	0.471
summaryOutput	0.737	0.013	0.750
testDataset	1.18	0.02	1.20
testFinalLRModel	0.298	0.015	0.313
testFinalModel	0.755	0.009	0.764
vectorOutput	0.734	0.007	0.741
vectorOutputMatrices	0.192	0.007	0.198