Back to the "Multiple platform build/check report" A  B  C  D [E] F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 166/553HostnameOS / ArchBUILDCHECKBUILD BIN
edgeR 2.6.12
Mark Robinson , Davis McCarthy , Yunshun Chen , Gordon Smyth
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/edgeR
Last Changed Rev: 68833 / Revision: 69725
Last Changed Date: 2012-08-26 21:32:27 -0700 (Sun, 26 Aug 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

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

Command output

* 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.

edgeR.Rcheck/00install.out:

* 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)

edgeR.Rcheck/edgeR-Ex.timings:

nameusersystemelapsed
DGEList0.0160.0000.015
adjustedProfileLik0.0120.0040.016
approx.expected.info0.1000.0040.107
betaApproxNBTest0.0000.0000.001
bin.dispersion2.2600.0042.265
binomTest0.0000.0000.002
calcNormFactors0.0080.0000.006
commonCondLogLikDerDelta0.0040.0000.003
condLogLikDerDelta0.0000.0000.001
condLogLikDerSize000
cpm0.0040.0000.003
cutWithMinN0.0000.0000.002
dglmStdResid0.0600.0040.060
dim0.0040.0000.003
dispBinTrend1.260.001.26
dispCoxReid0.1040.0000.101
dispCoxReidInterpolateTagwise0.2440.0040.246
dispCoxReidSplineTrend2.6600.0042.665
edgeRUsersGuide0.0080.0000.003
equalizeLibSizes0.2560.0000.256
estimateCommonDisp0.0480.0000.048
estimateExonGenewisedisp0.0400.0000.041
estimateGLMCommonDisp0.2160.0040.219
estimateGLMTagwiseDisp1.3560.0001.385
estimateGLMTrendedDisp1.0720.0001.105
estimatePs0.0040.0000.006
estimateSmoothing0.0240.0000.021
estimateTagwiseDisp0.1960.0000.203
estimateTrendedDisp1.5480.0001.616
exactTest0.0520.0000.051
expandAsMatrix000
getCounts0.0240.0000.021
getPriorN0.0040.0000.002
glmfit0.9680.0000.971
gof0.0600.0000.059
goodTuring0.0040.0000.006
logLikDerP0.0040.0000.002
maPlot0.0200.0000.019
maximizeInterpolant0.0040.0000.001
maximizeQuadratic0.0000.0000.001
meanvar0.2280.0040.232
mglm0.1240.0000.120
movingAverageByCol000
plotBCV1.6280.0041.632
plotExonUsage0.0080.0000.009
plotMDS.dge0.0120.0040.016
plotSmear0.7850.0000.780
predFC0.1640.0000.164
q2qnbinom0.1920.0000.193
readDGE000
spliceVariants0.0360.0000.039
splitIntoGroups0.0000.0000.002
subsetting0.0400.0040.043
systematicSubset0.0000.0000.001
thinCounts0.0000.0000.001
topTags0.0400.0000.041
weightedComLik0.0240.0000.022
weightedCondLogLikDerDelta0.0040.0000.003
zscoreNBinom000