BioC 2.10: CHECK report for edgeR on petty

Package: edgeR

Version: 2.6.12

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch edgeR_2.6.12.tar.gz

StartedAt: 2012-09-23 23:59:02 -0700 (Sun, 23 Sep 2012)

EndedAt: 2012-09-24 00:00:42 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 100.5 seconds

RetCode: 0

Status: OK

CheckDir: edgeR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/edgeR.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 sizes of PDF files under 'inst/doc' ... 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
  '/Users/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	0.017	0.001	0.019
adjustedProfileLik	0.024	0.004	0.028
approx.expected.info	0.081	0.001	0.083
betaApproxNBTest	0.001	0.001	0.001
bin.dispersion	2.620	0.007	2.629
binomTest	0.003	0.000	0.003
calcNormFactors	0.009	0.000	0.010
commonCondLogLikDerDelta	0.004	0.000	0.004
condLogLikDerDelta	0.002	0.001	0.002
condLogLikDerSize	0.001	0.000	0.001
cpm	0.003	0.001	0.004
cutWithMinN	0.006	0.000	0.007
dglmStdResid	0.090	0.004	0.094
dim	0.004	0.001	0.005
dispBinTrend	1.813	0.008	1.821
dispCoxReid	0.138	0.000	0.139
dispCoxReidInterpolateTagwise	0.359	0.003	0.362
dispCoxReidSplineTrend	3.654	0.006	3.660
edgeRUsersGuide	0.003	0.003	0.006
equalizeLibSizes	0.206	0.085	0.315
estimateCommonDisp	0.055	0.001	0.056
estimateExonGenewisedisp	0.077	0.000	0.077
estimateGLMCommonDisp	0.369	0.002	0.371
estimateGLMTagwiseDisp	1.468	0.005	1.473
estimateGLMTrendedDisp	1.097	0.001	1.097
estimatePs	0.006	0.000	0.006
estimateSmoothing	0.026	0.000	0.026
estimateTagwiseDisp	0.195	0.004	0.198
estimateTrendedDisp	2.359	0.071	2.450
exactTest	0.051	0.001	0.052
expandAsMatrix	0.000	0.001	0.000
getCounts	0.022	0.000	0.023
getPriorN	0.004	0.001	0.004
glmfit	1.176	0.003	1.180
gof	0.056	0.001	0.056
goodTuring	0.007	0.001	0.008
logLikDerP	0.002	0.000	0.003
maPlot	0.021	0.003	0.023
maximizeInterpolant	0.001	0.000	0.001
maximizeQuadratic	0.001	0.000	0.001
meanvar	0.263	0.005	0.270
mglm	0.040	0.002	0.042
movingAverageByCol	0.000	0.000	0.001
plotBCV	1.928	0.069	2.000
plotExonUsage	0.011	0.002	0.013
plotMDS.dge	0.015	0.003	0.018
plotSmear	0.754	0.153	0.912
predFC	0.189	0.002	0.192
q2qnbinom	0.168	0.052	0.222
readDGE	0.000	0.001	0.001
spliceVariants	0.045	0.000	0.046
splitIntoGroups	0.003	0.000	0.003
subsetting	0.051	0.002	0.053
systematicSubset	0	0	0
thinCounts	0.000	0.001	0.001
topTags	0.056	0.001	0.057
weightedComLik	0.027	0.001	0.028
weightedCondLogLikDerDelta	0.003	0.000	0.003
zscoreNBinom	0.001	0.001	0.001

Summary

Command output