BioC 3.0: CHECK report for PhenStat on oaxaca

Package: PhenStat

Version: 2.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PhenStat_2.0.0.tar.gz

StartedAt: 2015-04-10 02:08:02 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 02:10:58 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 176.7 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 --no-multiarch PhenStat_2.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/PhenStat.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘2.0.0’
* 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 ... [11s/12s] OK
* checking installed package size ... OK
* 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 ... [47s/48s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
qqplotRotatedResiduals 8.203  0.038   8.262
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [5s/5s]
 [6s/6s] 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

* 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	0.488	0.014	0.577
PhenList-class	0.537	0.008	0.595
PhenList	0.458	0.009	0.478
PhenTestResult-class	1.974	0.016	2.008
PhenTestResult	1.282	0.007	1.302
RRTest	0.311	0.003	0.314
TFDataset	0.639	0.010	0.649
boxplotResidualBatch	1.599	0.019	1.647
boxplotSexGenotype	0.176	0.004	0.210
boxplotSexGenotypeBatch	0.298	0.006	0.342
categoricalBarplot	0.483	0.007	0.510
checkDataset	0.106	0.002	0.114
classificationTag	1.602	0.010	1.654
dim	0.114	0.001	0.116
finalModel	1.393	0.005	1.415
finalTFModel	1.593	0.010	1.614
method	1.468	0.008	1.518
modelFormula	0.001	0.000	0.001
parserOutputSummary	1.601	0.013	1.622
parserOutputTFSummary	0.253	0.002	0.255
plotResidualPredicted	1.482	0.013	1.497
printTabStyle	0.003	0.000	0.003
qqplotGenotype	1.471	0.013	1.485
qqplotRandomEffects	1.587	0.007	1.597
qqplotRotatedResiduals	8.203	0.038	8.262
recommendMethod	0.824	0.010	0.835
scatterplotGenotypeWeight	0.222	0.003	0.227
scatterplotSexGenotypeBatch	0.208	0.005	0.213
startModel	1.147	0.011	1.166
startTFModel	1.328	0.009	1.348
summaryOutput	1.871	0.034	1.909
testDataset	3.088	0.035	3.137
testFinalModel	1.724	0.014	1.743
vectorOutput	1.948	0.023	1.992
vectorOutputMatrices	0.471	0.011	0.483