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BioC 2.14: CHECK report for PhenStat on morelia

This page was generated on 2014-10-08 09:07:16 -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: 2014-10-08 00:40:06 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 00:41:36 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 89.7 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-darwin13.1.0 (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 ... [4s/4s] 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 ... [36s/37s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
qqplotRotatedResiduals 7.264   0.04   7.342
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [2s/2s]
 [2s/2s] 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
FisherExactTest0.6720.0180.699
PhenList-class0.4080.0080.417
PhenList0.4900.0080.500
PhenTestResult-class1.8320.0271.859
PhenTestResult1.2020.0091.215
boxplotResidualBatch1.5180.0071.527
boxplotSexGenotype0.1810.0050.187
boxplotSexGenotypeBatch0.2740.0070.281
categoricalBarplot0.4820.0060.489
checkDataset0.0920.0010.094
classificationTag1.3760.0061.388
dim0.1130.0020.115
finalModel1.2370.0081.247
method1.4300.0041.436
modelFormula0.0010.0000.001
parserOutputSummary1.4010.0101.412
plotResidualPredicted1.2930.0041.330
qqplotGenotype1.3800.0071.395
qqplotRandomEffects1.4370.0141.453
qqplotRotatedResiduals7.2640.0407.342
scatterplotGenotypeWeight0.2200.0051.241
startModel1.0620.0051.069
summaryOutput1.7910.0151.808
testDataset2.8880.0242.921
testFinalModel1.5570.0061.569
vectorOutput1.8240.0101.835
vectorOutputMatrices0.4700.0030.479