BioC 2.10: CHECK report for edgeR on puck5

Package: edgeR

Version: 2.6.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_2.6.0.tar.gz

StartedAt: 2012-04-01 00:44:49 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 00:45:46 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 56.7 seconds

RetCode: 0

Status: OK

CheckDir: edgeR.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/edgeR.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'edgeR/DESCRIPTION' ... OK
* this is package 'edgeR' version '2.6.0'
* 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 '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 installed files from 'inst/doc' ... 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

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

* DONE (edgeR)

name	user	system	elapsed
DGEList	0.012	0.000	0.012
adjustedProfileLik	0.008	0.004	0.011
approx.expected.info	0.060	0.000	0.061
betaApproxNBTest	0.000	0.000	0.001
bin.dispersion	1.380	0.004	1.385
binomTest	0.004	0.000	0.001
calcNormFactors	0.004	0.000	0.002
commonCondLogLikDerDelta	0.000	0.000	0.002
condLogLikDerDelta	0.004	0.000	0.000
condLogLikDerSize	0	0	0
cpm	0.000	0.000	0.002
cutWithMinN	0.000	0.000	0.002
dglmStdResid	0.048	0.000	0.048
dim	0.004	0.000	0.003
dispBinTrend	0.500	0.004	0.511
dispCoxReid	0.040	0.000	0.044
dispCoxReidInterpolateTagwise	0.152	0.000	0.153
dispCoxReidSplineTrend	1.016	0.000	1.022
equalizeLibSizes	0.152	0.000	0.151
estimateCommonDisp	0.040	0.000	0.042
estimateExonGenewisedisp	0.036	0.000	0.039
estimateGLMCommonDisp	0.112	0.000	0.113
estimateGLMTagwiseDisp	0.660	0.004	0.667
estimateGLMTrendedDisp	0.452	0.004	0.462
estimatePs	0.008	0.000	0.005
estimateSmoothing	0.020	0.000	0.021
estimateTagwiseDisp	0.164	0.000	0.163
estimateTrendedDisp	1.280	0.004	1.286
exactTest	0.044	0.000	0.042
expandAsMatrix	0	0	0
getCounts	0.020	0.000	0.018
getPriorN	0.000	0.000	0.002
glmfit	0.460	0.004	0.468
gof	0.028	0.000	0.031
goodTuring	0.004	0.000	0.005
logLikDerP	0.004	0.000	0.002
maPlot	0.016	0.000	0.019
maximizeInterpolant	0.000	0.000	0.001
maximizeQuadratic	0	0	0
meanvar	0.200	0.000	0.198
mglm	0.036	0.000	0.035
movingAverageByCol	0	0	0
plotBCV	1.412	0.004	1.422
plotExonUsage	0.012	0.000	0.009
plotMDS.dge	0.012	0.000	0.013
plotSmear	0.688	0.000	0.688
predFC	0.080	0.000	0.081
q2qnbinom	0.100	0.000	0.101
readDGE	0	0	0
spliceVariants	0.024	0.000	0.024
splitIntoGroups	0.004	0.000	0.002
subsetting	0.040	0.000	0.041
systematicSubset	0	0	0
thinCounts	0	0	0
topTags	0.036	0.000	0.035
weightedComLik	0.02	0.00	0.02
weightedCondLogLikDerDelta	0.004	0.000	0.002
zscoreNBinom	0.000	0.000	0.001

Summary

Command output