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Package 122/436HostnameOS / ArchBUILDCHECKBUILD BIN
edgeR 2.1.12
Mark Robinson , Davis McCarthy , Gordon Smyth
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edgeR
Last Changed Rev: 52933 / Revision: 53255
Last Changed Date: 2011-02-16 20:39:23 -0800 (Wed, 16 Feb 2011)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ WARNINGS ] OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK  WARNINGS  OK 

Summary

Package: edgeR
Version: 2.1.12
Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings edgeR_2.1.12.tar.gz
StartedAt: 2011-02-24 17:51:03 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 17:51:56 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 53.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: edgeR.Rcheck
Warnings: 3

Command output

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/edgeR.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'edgeR/DESCRIPTION' ... OK
* this is package 'edgeR' version '2.1.12'
* 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 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 ... WARNING
dispCoxReid:
  function(y, design, offset, interval, tol, ...)
dispCoxReid.DGEList:
  function(y, design, offset, interval, tol)

dispCoxReid:
  function(y, design, offset, interval, tol, ...)
dispCoxReid.default:
  function(y, design, offset, interval, tol)

See section 'Generic functions and methods' of the 'Writing R
Extensions' manual.
* 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 ... WARNING
Undocumented code objects:
  dispCoxReid dispCoxReid.DGEList dispCoxReid.default getOffsets
  mglmOneGroup.DGEList mglmOneGroup.default
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'mglm':
mglmOneGroup
  Code: function(y, dispersion = 0, offset = NULL, maxit = 50, trace =
                 FALSE)
  Docs: function(y, dispersion = 0, offset = 0, maxit = 50, trace =
                 FALSE)
  Mismatches in argument default values:
    Name: 'offset' Code: NULL Docs: 0

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'mseq-Tests.R'
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 3 warnings, see
  'E:/biocbld/bbs-2.8-bioc/meat/edgeR.Rcheck/00check.log'
for details

edgeR.Rcheck/00install.out:

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

* DONE (edgeR)

edgeR.Rcheck/edgeR-Ex.timings:

nameusersystemelapsed
DGEList0.020.000.02
approx.expected.info0.090.000.09
betaApproxNBTest000
calcNormFactors000
commonCondLogLikDerDelta000
condLogLikDerDelta000
condLogLikDerSize000
dglmStdResid0.080.000.08
dim0.010.000.01
equalizeLibSizes0.190.000.21
estimateCRDisp0.870.000.87
estimateCommonDisp0.070.000.06
estimatePs0.010.000.02
estimateSmoothing0.030.000.03
estimateTagwiseDisp0.220.000.22
exactTest0.050.000.05
expandAsMatrix000
getCounts0.010.000.01
glmfit0.050.000.05
goodTuring0.020.000.01
logLikDerP000
maPlot0.040.000.05
meanvar0.330.000.45
mglm0.050.000.05
plotMDS.dge8.480.028.63
plotSmear0.910.010.93
q2qnbinom0.140.000.14
readDGE000
splitIntoGroups000
subsetting0.050.000.07
topTags0.060.000.06
weightedComLik0.050.000.05
weightedCondLogLikDerDelta000