BioC 3.0: CHECK report for PhenStat on zin1

Package: PhenStat

Version: 2.0.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings PhenStat_2.0.0.tar.gz

StartedAt: 2015-04-10 02:57:08 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 02:59:23 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 134.9 seconds

RetCode: 0

Status:  OK

CheckDir: PhenStat.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings PhenStat_2.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/PhenStat.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ... [9s/10s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [33s/35s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
qqplotRotatedResiduals 5.104  0.028   5.161
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [4s/4s]
 [5s/5s] 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	0.344	0.008	0.356
PhenList-class	0.408	0.008	0.418
PhenList	0.328	0.004	0.793
PhenTestResult-class	1.424	0.012	1.472
PhenTestResult	0.932	0.004	0.938
RRTest	0.252	0.000	0.251
TFDataset	0.544	0.008	0.552
boxplotResidualBatch	1.028	0.004	1.034
boxplotSexGenotype	0.136	0.000	0.133
boxplotSexGenotypeBatch	0.344	0.008	0.675
categoricalBarplot	0.336	0.004	0.338
checkDataset	0.072	0.004	0.075
classificationTag	1.036	0.004	1.041
dim	0.080	0.000	0.081
finalModel	0.944	0.004	0.948
finalTFModel	1.220	0.008	1.294
method	1.188	0.004	1.220
modelFormula	0.004	0.000	0.000
parserOutputSummary	1.024	0.000	1.030
parserOutputTFSummary	0.204	0.000	0.207
plotResidualPredicted	1.021	0.012	1.036
printTabStyle	0.000	0.000	0.001
qqplotGenotype	0.992	0.004	0.996
qqplotRandomEffects	0.984	0.000	0.987
qqplotRotatedResiduals	5.104	0.028	5.161
recommendMethod	0.548	0.008	0.651
scatterplotGenotypeWeight	0.188	0.004	0.206
scatterplotSexGenotypeBatch	0.152	0.008	0.180
startModel	0.808	0.016	0.897
startTFModel	0.956	0.008	0.966
summaryOutput	1.432	0.000	1.437
testDataset	2.040	0.024	2.198
testFinalModel	1.124	0.008	1.138
vectorOutput	1.289	0.004	1.299
vectorOutputMatrices	0.316	0.000	0.317