BioC 2.14: CHECK report for PhenStat on petty

Package: PhenStat

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PhenStat_1.2.0.tar.gz

StartedAt: 2014-10-07 23:26:49 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:29:16 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 146.3 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 --no-multiarch PhenStat_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/PhenStat.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.2.0’
* 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 ... [6s/7s] 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 ... [59s/60s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
qqplotRotatedResiduals 10.811  0.082  11.201
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [3s/3s]
 [4s/4s] 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

* 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	0.892	0.020	0.919
PhenList-class	0.537	0.010	0.552
PhenList	0.660	0.007	0.668
PhenTestResult-class	3.098	0.045	3.155
PhenTestResult	2.127	0.013	2.156
boxplotResidualBatch	2.501	0.011	2.625
boxplotSexGenotype	0.262	0.005	0.268
boxplotSexGenotypeBatch	0.457	0.007	0.468
categoricalBarplot	0.719	0.005	0.730
checkDataset	0.145	0.002	0.151
classificationTag	2.493	0.008	2.544
dim	0.159	0.002	0.162
finalModel	1.974	0.010	1.992
method	2.337	0.005	2.352
modelFormula	0.001	0.000	0.001
parserOutputSummary	2.441	0.009	2.460
plotResidualPredicted	2.418	0.007	2.432
qqplotGenotype	2.384	0.009	2.403
qqplotRandomEffects	2.369	0.010	2.416
qqplotRotatedResiduals	10.811	0.082	11.201
scatterplotGenotypeWeight	0.352	0.007	0.366
startModel	1.894	0.005	1.927
summaryOutput	3.121	0.037	3.220
testDataset	4.877	0.047	4.980
testFinalModel	2.693	0.008	2.732
vectorOutput	3.032	0.015	3.080
vectorOutputMatrices	0.710	0.005	0.717