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Package 163/609HostnameOS / ArchBUILDCHECKBUILD BIN
DEXSeq 1.4.0
Alejandro Reyes
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/DEXSeq
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: DEXSeq
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DEXSeq_1.4.0.tar.gz
StartedAt: 2013-03-24 23:15:57 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 23:18:39 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 162.0 seconds
RetCode: 0
Status:  OK 
CheckDir: DEXSeq.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/DEXSeq.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'DEXSeq/DESCRIPTION' ... OK
* this is package 'DEXSeq' version '1.4.0'
* 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 whether package 'DEXSeq' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 for unstated 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 examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
read.HTSeqCounts        29.195  1.649  31.362
makeCompleteDEUAnalysis 17.591  2.984  21.881
estimateDispersions     14.744  2.215  17.582
fitDispersionFunction   10.221  1.943  12.687
testGeneForDEU           9.151  1.525  11.025
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

DEXSeq.Rcheck/00install.out:

* installing *source* package 'DEXSeq' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'DEXSeq.Rnw' 
** testing if installed package can be loaded

* DONE (DEXSeq)

DEXSeq.Rcheck/DEXSeq-Ex.timings:

nameusersystemelapsed
DEUresultTable000
DEXSeqHTML000
ExonCountSet-class0.0000.0000.001
countTableForGene0.2470.0200.266
counts0.0160.0030.020
design0.0210.0040.026
estimateDispersions14.744 2.21517.582
estimateExonDispersionsForModelFrame0.2290.0480.295
estimateSizeFactors0.0410.0070.049
estimatelog2FoldChanges000
exonIDs0.0180.0060.024
fitDispersionFunction10.221 1.94312.687
geneCountTable0.0420.0040.047
geneIDs0.0270.0050.031
makeCompleteDEUAnalysis17.591 2.98421.881
modelFrameForGene0.0250.0050.032
newExonCountSet0.2560.0290.288
perGeneQValue000
plotDEXSeq000
read.HTSeqCounts29.195 1.64931.362
sizeFactors0.0440.0040.048
subsetByGenes0.0510.0060.057
testForDEU000
testGeneForDEU 9.151 1.52511.025