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BioC 2.14: CHECK report for PhenStat on petty

This page was generated on 2014-10-08 09:01:32 -0700 (Wed, 08 Oct 2014).

Package 581/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhenStat 1.2.0
Natasha Karp
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/PhenStat
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

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

Command output

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


* 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

PhenStat.Rcheck/00install.out:

* 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)

PhenStat.Rcheck/PhenStat-Ex.timings:

nameusersystemelapsed
FisherExactTest0.8920.0200.919
PhenList-class0.5370.0100.552
PhenList0.6600.0070.668
PhenTestResult-class3.0980.0453.155
PhenTestResult2.1270.0132.156
boxplotResidualBatch2.5010.0112.625
boxplotSexGenotype0.2620.0050.268
boxplotSexGenotypeBatch0.4570.0070.468
categoricalBarplot0.7190.0050.730
checkDataset0.1450.0020.151
classificationTag2.4930.0082.544
dim0.1590.0020.162
finalModel1.9740.0101.992
method2.3370.0052.352
modelFormula0.0010.0000.001
parserOutputSummary2.4410.0092.460
plotResidualPredicted2.4180.0072.432
qqplotGenotype2.3840.0092.403
qqplotRandomEffects2.3690.0102.416
qqplotRotatedResiduals10.811 0.08211.201
scatterplotGenotypeWeight0.3520.0070.366
startModel1.8940.0051.927
summaryOutput3.1210.0373.220
testDataset4.8770.0474.980
testFinalModel2.6930.0082.732
vectorOutput3.0320.0153.080
vectorOutputMatrices0.7100.0050.717