BioC 3.0: CHECK report for PhenStat on perceval

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 04:46:40 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 04:50:17 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 216.9 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-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 ‘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 ... [15s/16s] 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 ... [49s/50s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
qqplotRotatedResiduals 7.377  0.064    7.47
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [7s/7s]
 [7s/7s] 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	0.432	0.018	0.450
PhenList-class	0.582	0.008	0.591
PhenList	0.359	0.007	0.367
PhenTestResult-class	2.050	0.025	2.081
PhenTestResult	1.542	0.012	1.554
RRTest	0.159	0.002	0.161
TFDataset	0.888	0.030	0.918
boxplotResidualBatch	1.503	0.018	1.530
boxplotSexGenotype	0.211	0.007	0.246
boxplotSexGenotypeBatch	0.300	0.010	0.695
categoricalBarplot	0.439	0.006	0.475
checkDataset	0.104	0.001	0.106
classificationTag	1.684	0.004	1.691
dim	0.101	0.002	0.103
finalModel	1.283	0.006	1.295
finalTFModel	1.698	0.011	1.709
method	1.637	0.008	1.645
modelFormula	0.001	0.001	0.001
parserOutputSummary	1.699	0.004	1.707
parserOutputTFSummary	0.258	0.002	0.261
plotResidualPredicted	1.387	0.007	1.404
printTabStyle	0.002	0.001	0.002
qqplotGenotype	1.658	0.005	1.669
qqplotRandomEffects	1.404	0.006	1.423
qqplotRotatedResiduals	7.377	0.064	7.470
recommendMethod	0.937	0.012	0.955
scatterplotGenotypeWeight	0.210	0.006	0.238
scatterplotSexGenotypeBatch	0.182	0.006	0.205
startModel	1.162	0.020	1.183
startTFModel	1.387	0.012	1.398
summaryOutput	1.797	0.027	1.829
testDataset	2.953	0.014	2.995
testFinalModel	1.590	0.016	1.606
vectorOutput	1.847	0.023	1.875
vectorOutputMatrices	0.396	0.004	0.401