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Package 136/462HostnameOS / ArchBUILDCHECKBUILD BIN
edgeR 2.3.13
Mark Robinson , Davis McCarthy , Gordon Smyth
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edgeR
Last Changed Rev: 55347 / Revision: 55359
Last Changed Date: 2011-05-08 23:31:05 -0700 (Sun, 08 May 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: edgeR
Version: 2.3.13
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_2.3.13.tar.gz
StartedAt: 2011-05-09 12:16:54 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 12:18:27 -0700 (Mon, 09 May 2011)
EllapsedTime: 92.8 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 2.14.0 Under development (unstable) (2011-04-18 r55504)
* 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 ‘2.3.13’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
DGEList0.0160.0000.014
adjustedProfileLik0.0080.0080.021
approx.expected.info0.0840.0000.086
betaApproxNBTest000
bin.dispersion6.300.006.46
binomTest0.0000.0000.001
calcNormFactors0.0080.0000.006
commonCondLogLikDerDelta0.0040.0000.004
condLogLikDerDelta0.0000.0000.001
condLogLikDerSize000
cutWithMinN0.0040.0000.003
dglmStdResid0.0520.0040.058
dim0.0000.0000.003
dispBinTrend3.460.003.46
dispCoxReid0.1240.0000.124
dispCoxReidInterpolateTagwise0.4200.0000.418
dispCoxReidSplineTrend4.2360.0004.243
equalizeLibSizes0.1810.0000.183
estimateCRDisp3.4960.0083.507
estimateCommonDisp0.0640.0000.063
estimateGLMCommonDisp0.2240.0000.224
estimateGLMTagwiseDisp5.0360.0005.039
estimateGLMTrendedDisp4.5160.0004.518
estimatePs0.0080.0000.009
estimateSmoothing0.0320.0000.034
estimateTagwiseDisp0.2000.0040.203
exactTest0.0520.0000.053
expandAsMatrix0.0000.0000.001
getCounts0.0040.0000.002
getOffsets0.0040.0000.003
getPriorN0.0000.0040.003
glmfit0.0600.0000.062
gof0.0440.0000.041
goodTuring0.0080.0000.006
logLikDerP0.0040.0000.003
maPlot0.0120.0040.016
maximizeInterpolant0.0040.0000.004
meanvar0.3800.0000.377
mglm0.0440.0000.046
movingAverageByCol0.0000.0000.001
plotMDS.dge8.9290.0368.974
plotSmear0.8400.0040.844
q2qnbinom0.1200.0040.122
readDGE000
splitIntoGroups0.0040.0000.003
subsetting0.0720.0000.073
systematicSubset000
thinCounts000
topTags0.0680.0000.066
weightedComLik0.0320.0000.033
weightedCondLogLikDerDelta0.0040.0000.003