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Package 140/479HostnameOS / ArchBUILDCHECKBUILD BIN
edgeR 2.3.29
Mark Robinson , Davis McCarthy , Gordon Smyth
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edgeR
Last Changed Rev: 56416 / Revision: 56603
Last Changed Date: 2011-06-27 01:21:02 -0700 (Mon, 27 Jun 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: edgeR
Version: 2.3.29
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch edgeR_2.3.29.tar.gz
StartedAt: 2011-07-07 02:46:19 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 02:48:06 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 106.1 seconds
RetCode: 0
Status:  OK 
CheckDir: edgeR.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/edgeR.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* 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 '2.3.29'
* 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 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 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 ... 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 sizes of PDF files under '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

edgeR.Rcheck/00install.out:

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

* DONE (edgeR)

edgeR.Rcheck/edgeR-Ex.timings:

nameusersystemelapsed
DGEList0.0190.0020.021
adjustedProfileLik0.0160.0030.019
approx.expected.info0.1390.0010.146
betaApproxNBTest0.0010.0000.001
bin.dispersion3.4400.0143.481
binomTest0.0030.0000.003
calcNormFactors0.0050.0000.006
commonCondLogLikDerDelta0.0060.0000.006
condLogLikDerDelta0.0030.0000.003
condLogLikDerSize0.0000.0010.001
cpm0.0040.0000.004
cutWithMinN0.0340.0000.033
dglmStdResid0.0770.0020.079
dim0.0040.0000.005
dispBinTrend1.1010.0141.132
dispCoxReid0.0830.0000.085
dispCoxReidInterpolateTagwise0.3880.0030.396
dispCoxReidSplineTrend2.2990.0062.309
equalizeLibSizes0.270.080.35
estimateCRDisp0.8500.0050.866
estimateCommonDisp0.0890.0000.090
estimateGLMCommonDisp0.2390.0020.242
estimateGLMTagwiseDisp1.4060.0061.430
estimateGLMTrendedDisp0.9650.0030.978
estimatePs0.0100.0000.012
estimateSmoothing0.0510.0010.052
estimateTagwiseDisp0.2860.0080.299
exactTest0.0730.0000.075
expandAsMatrix0.0010.0000.001
getCounts0.0030.0000.003
getOffset0.0030.0000.003
getPriorN0.0040.0000.003
glmfit0.8870.0070.903
gof0.0520.0040.055
goodTuring0.0090.0010.009
logLikDerP0.0030.0000.004
maPlot0.0280.0010.030
maximizeInterpolant0.0030.0000.003
meanvar0.4330.0120.452
mglm0.0590.0010.059
movingAverageByCol0.0010.0000.001
plotMDS.dge2.5350.5103.096
plotSmear1.0710.1971.323
q2qnbinom0.1530.0460.200
readDGE000
splitIntoGroups0.0040.0000.004
subsetting0.0990.0040.103
systematicSubset0.0000.0010.000
thinCounts0.0010.0000.001
topTags0.0900.0020.093
weightedComLik0.0470.0010.050
weightedCondLogLikDerDelta0.0050.0000.005