BioC 2.10: CHECK report for edgeR on lamb2

Package: edgeR

Version: 2.6.12

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_2.6.12.tar.gz

StartedAt: 2012-09-24 00:34:35 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 00:35:54 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 78.9 seconds

RetCode: 0

Status: OK

CheckDir: edgeR.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/edgeR.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘2.6.12’
* 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 ... NOTE
mglmLevenberg: warning in glmnb.fit(X = X, y = z, dispersion =
  dispersion[i], offset = offset[i, ], start = start[i, ]): partial
  argument match of 'start' to 'start.method'
* 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’ ...416c416
< [1] 0.53374778 0.20168294 4.18933146 0.69542655 0.00796757
---
> [1] 0.53374778 0.20168294 4.18933184 0.69542655 0.00796757
442,446c442,446
< Gene1 3.128148 16.522832 99.713625
< Gene2 4.522517  5.858801  8.671818
< Gene3 1.169726  2.402414  5.637468
< Gene4 4.176370  4.709091  6.066636
< Gene5 2.072116  3.834708  8.108178
---
> Gene1 3.128147 16.522846 99.713802
> Gene2 4.522480  5.858800  8.671883
> Gene3 1.169671  2.402414  5.637736
> Gene4 4.176397  4.709091  6.066597
> Gene5 2.072114  3.834707  8.108180
 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

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/edgeR.Rcheck/00check.log’
for details.

* 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	0.016	0.000	0.015
adjustedProfileLik	0.012	0.004	0.016
approx.expected.info	0.100	0.004	0.107
betaApproxNBTest	0.000	0.000	0.001
bin.dispersion	2.260	0.004	2.265
binomTest	0.000	0.000	0.002
calcNormFactors	0.008	0.000	0.006
commonCondLogLikDerDelta	0.004	0.000	0.003
condLogLikDerDelta	0.000	0.000	0.001
condLogLikDerSize	0	0	0
cpm	0.004	0.000	0.003
cutWithMinN	0.000	0.000	0.002
dglmStdResid	0.060	0.004	0.060
dim	0.004	0.000	0.003
dispBinTrend	1.26	0.00	1.26
dispCoxReid	0.104	0.000	0.101
dispCoxReidInterpolateTagwise	0.244	0.004	0.246
dispCoxReidSplineTrend	2.660	0.004	2.665
edgeRUsersGuide	0.008	0.000	0.003
equalizeLibSizes	0.256	0.000	0.256
estimateCommonDisp	0.048	0.000	0.048
estimateExonGenewisedisp	0.040	0.000	0.041
estimateGLMCommonDisp	0.216	0.004	0.219
estimateGLMTagwiseDisp	1.356	0.000	1.385
estimateGLMTrendedDisp	1.072	0.000	1.105
estimatePs	0.004	0.000	0.006
estimateSmoothing	0.024	0.000	0.021
estimateTagwiseDisp	0.196	0.000	0.203
estimateTrendedDisp	1.548	0.000	1.616
exactTest	0.052	0.000	0.051
expandAsMatrix	0	0	0
getCounts	0.024	0.000	0.021
getPriorN	0.004	0.000	0.002
glmfit	0.968	0.000	0.971
gof	0.060	0.000	0.059
goodTuring	0.004	0.000	0.006
logLikDerP	0.004	0.000	0.002
maPlot	0.020	0.000	0.019
maximizeInterpolant	0.004	0.000	0.001
maximizeQuadratic	0.000	0.000	0.001
meanvar	0.228	0.004	0.232
mglm	0.124	0.000	0.120
movingAverageByCol	0	0	0
plotBCV	1.628	0.004	1.632
plotExonUsage	0.008	0.000	0.009
plotMDS.dge	0.012	0.004	0.016
plotSmear	0.785	0.000	0.780
predFC	0.164	0.000	0.164
q2qnbinom	0.192	0.000	0.193
readDGE	0	0	0
spliceVariants	0.036	0.000	0.039
splitIntoGroups	0.000	0.000	0.002
subsetting	0.040	0.004	0.043
systematicSubset	0.000	0.000	0.001
thinCounts	0.000	0.000	0.001
topTags	0.040	0.000	0.041
weightedComLik	0.024	0.000	0.022
weightedCondLogLikDerDelta	0.004	0.000	0.003
zscoreNBinom	0	0	0

Summary

Command output