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Package 151/514HostnameOS / ArchBUILDCHECKBUILD BIN
edgeR 2.4.6
Mark Robinson , Davis McCarthy , Yunshun Chen , Gordon Smyth
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/edgeR
Last Changed Rev: 63835 / Revision: 64395
Last Changed Date: 2012-03-13 15:36:09 -0700 (Tue, 13 Mar 2012)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: edgeR
Version: 2.4.6
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_2.4.6.tar.gz
StartedAt: 2012-03-24 00:11:11 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 00:12:15 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 63.3 seconds
RetCode: 0
Status:  OK 
CheckDir: edgeR.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/edgeR.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘edgeR/DESCRIPTION’ ... OK
* this is package ‘edgeR’ version ‘2.4.6’
* 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 ‘edgeR’ 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘edgeR-Tests.R’
  Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-Tests.Rout.save’ ... OK
 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

edgeR.Rcheck/00install.out:

* installing *source* package ‘edgeR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘edgeR.Rnw’ 
** testing if installed package can be loaded

* DONE (edgeR)

edgeR.Rcheck/edgeR-Ex.timings:

nameusersystemelapsed
DGEList0.0160.0000.016
adjustedProfileLik0.0160.0000.016
approx.expected.info0.1280.0000.129
betaApproxNBTest000
bin.dispersion1.9480.0001.977
binomTest0.0040.0000.002
calcNormFactors0.0040.0000.003
commonCondLogLikDerDelta0.0040.0000.003
condLogLikDerDelta0.0000.0000.001
condLogLikDerSize000
cpm0.0000.0000.003
cutWithMinN0.0000.0000.002
dglmStdResid0.060.000.06
dim0.0040.0000.003
dispBinTrend0.7400.0000.741
dispCoxReid0.0560.0000.055
dispCoxReidInterpolateTagwise0.2080.0000.209
dispCoxReidSplineTrend1.5800.0041.581
equalizeLibSizes0.2440.0040.252
estimateCommonDisp0.0560.0000.055
estimateExonGenewisedisp0.0760.0000.076
estimateGLMCommonDisp0.160.000.16
estimateGLMTagwiseDisp0.9160.0040.917
estimateGLMTrendedDisp0.5960.0080.603
estimatePs0.0080.0000.008
estimateSmoothing0.0280.0000.030
estimateTagwiseDisp0.2600.0000.261
exactTest0.0760.0000.078
expandAsMatrix000
getCounts0.0200.0000.023
getPriorN0.0000.0000.002
glmfit0.5120.0000.512
gof0.0360.0000.038
goodTuring0.0080.0000.008
logLikDerP0.0040.0000.002
maPlot0.0160.0040.017
maximizeInterpolant0.0000.0000.002
meanvar0.3120.0000.319
mglm0.1120.0000.114
movingAverageByCol0.0040.0000.001
plotExonUsage0.0080.0000.008
plotMDS.dge0.0120.0000.013
plotSmear0.7040.0000.702
q2qnbinom0.1320.0000.133
readDGE000
spliceVariants0.0240.0040.028
splitIntoGroups0.0000.0000.002
subsetting0.0520.0000.052
systematicSubset0.0000.0000.001
thinCounts0.0000.0000.001
topTags0.0440.0000.043
weightedComLik0.0320.0000.029
weightedCondLogLikDerDelta0.0040.0000.003