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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: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings edgeR_2.3.13.tar.gz
StartedAt: 2011-05-09 16:36:21 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 16:38:40 -0700 (Mon, 09 May 2011)
EllapsedTime: 139.4 seconds
RetCode: 0
Status:  OK  
CheckDir: edgeR.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/edgeR.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
DGEList0.010.000.02
adjustedProfileLik0.020.000.03
approx.expected.info0.080.000.08
betaApproxNBTest000
bin.dispersion6.110.006.11
binomTest000
calcNormFactors0.010.000.01
commonCondLogLikDerDelta000
condLogLikDerDelta000
condLogLikDerSize000
cutWithMinN000
dglmStdResid0.060.000.07
dim000
dispBinTrend3.180.023.18
dispCoxReid0.110.000.11
dispCoxReidInterpolateTagwise0.380.000.37
dispCoxReidSplineTrend3.750.003.77
equalizeLibSizes0.150.000.16
estimateCRDisp3.310.013.32
estimateCommonDisp0.070.000.07
estimateGLMCommonDisp0.20.00.2
estimateGLMTagwiseDisp4.920.004.92
estimateGLMTrendedDisp4.350.004.34
estimatePs000
estimateSmoothing0.030.000.03
estimateTagwiseDisp0.190.000.19
exactTest0.050.000.05
expandAsMatrix000
getCounts000
getOffsets000
getPriorN0.010.000.01
glmfit0.050.000.05
gof0.050.000.05
goodTuring000
logLikDerP0.010.000.01
maPlot0.020.020.03
maximizeInterpolant000
meanvar0.310.000.31
mglm0.050.000.05
movingAverageByCol000
plotMDS.dge7.840.017.88
plotSmear0.800.000.79
q2qnbinom0.170.000.18
readDGE000
splitIntoGroups000
subsetting0.080.000.07
systematicSubset000
thinCounts000
topTags0.060.000.07
weightedComLik0.030.000.03
weightedCondLogLikDerDelta000