BioC 3.5: CHECK report for PhenStat on toluca2

Package: PhenStat

Version: 2.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PhenStat_2.9.0.tar.gz

StartedAt: 2017-04-23 07:56:15 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 07:58:29 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 134.2 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_2.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/PhenStat.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘2.9.0’
* 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
Examples with CPU or elapsed time > 5s
                        user system elapsed
qqplotRotatedResiduals 5.566   0.04   5.672
* 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	0.552	0.016	0.571
JSONOutput	2.727	0.043	2.791
LRDataset	0.140	0.004	0.144
PhenList-class	0.341	0.002	0.344
PhenList	0.370	0.003	0.373
PhenTestResult-class	1.849	0.032	1.892
PhenTestResult	0.609	0.005	0.614
RRTest	0.281	0.008	0.297
TFDataset	0.505	0.010	0.515
boxplotResidualBatch	0.800	0.014	0.815
boxplotSexGenotype	0.128	0.002	0.132
boxplotSexGenotypeBatch	0.215	0.002	0.221
boxplotSexGenotypeBatchAdjusted	0.117	0.001	0.120
boxplotSexGenotypeResult	1.022	0.018	1.048
boxplotSexGenotypeWeightBatchAdjusted	0.119	0.001	0.122
categoricalBarplot	0.303	0.006	0.315
checkDataset	0.080	0.001	0.081
classificationTag	0.932	0.010	0.950
determiningLambda	0.638	0.210	0.851
dim	0.082	0.001	0.083
finalLRModel	0.886	0.012	0.911
finalModel	0.601	0.009	0.612
finalTFModel	0.982	0.011	0.999
htestPhenStat-class	0.302	0.010	0.313
modelFormula	0.001	0.000	0.001
modelFormulaLR	0.000	0.000	0.001
parserOutputSummary	0.762	0.011	0.780
parserOutputSummaryLR	0.642	0.013	0.663
parserOutputTFSummary	0.559	0.002	0.563
performReverseTransformation	0.001	0.000	0.001
performTransformation	0.001	0.000	0.001
plotResidualPredicted	0.797	0.006	0.809
printLROutput	0.474	0.012	0.491
printTabStyle	0.002	0.000	0.002
qqplotGenotype	0.749	0.004	0.774
qqplotRandomEffects	0.766	0.004	0.820
qqplotRotatedResiduals	5.566	0.040	5.672
recommendMethod	0.436	0.003	0.443
scatterplotGenotypeWeight	0.339	0.007	0.350
scatterplotGenotypeWeightResult	0.937	0.014	0.957
scatterplotSexGenotypeBatch	0.140	0.004	0.148
scatterplotSexGenotypeBatchResult	0.930	0.010	0.949
startLRModel	0.378	0.007	0.386
startModel	0.362	0.002	0.365
startTFModel	0.681	0.008	0.690
summaryOutput	1.100	0.016	1.142
testDataset	1.458	0.017	1.476
testFinalLRModel	0.449	0.024	0.473
testFinalModel	0.923	0.007	0.931
vectorOutput	1.274	0.015	1.297
vectorOutputMatrices	0.363	0.005	0.370