Package: MassArray

Version: 1.5.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings MassArray_1.5.0.tar.gz

StartedAt: 2011-05-09 13:10:31 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 13:11:42 -0700 (Mon, 09 May 2011)

EllapsedTime: 70.3 seconds

RetCode: 0

Status:  OK

CheckDir: MassArray.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/MassArray.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MassArray/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MassArray’ version ‘1.5.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘MassArray’ 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 examples ... 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 ‘MassArray’ ...
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘MassArray.Rnw’ 
** testing if installed package can be loaded

* DONE (MassArray)

name	user	system	elapsed
MassArray.example.data	0.020	0.000	0.017
MassArrayData-class	0.000	0.000	0.001
MassArrayFragment-class	0.000	0.000	0.001
MassArrayPeak-class	0.004	0.000	0.001
MassArraySpectrum-class	0.000	0.000	0.001
ampliconPrediction	2.772	0.000	2.771
analyzeCpGs	0.240	0.004	0.242
bisConvert	0	0	0
calcMW	0.004	0.000	0.001
calcMeth	0.012	0.000	0.013
calcPercentAdduct	0.076	0.000	0.077
calcPercentConversion	0.052	0.000	0.054
combine	7.080	0.024	7.136
convControl	0.028	0.000	0.031
countCGs	0	0	0
createWiggle	0.012	0.000	0.012
estimatePrimerDimer	0.100	0.000	0.102
evaluateSNPs	29.106	0.024	29.315
expandSequence	0.000	0.000	0.001
findCollisions	0	0	0
findFragments	0.016	0.000	0.016
findPeaks	0	0	0
identifySNPs	0.036	0.000	0.034
inSilicoFragmentation	0.012	0.000	0.011
isAssayable	0	0	0
numCollisions	0	0	0
plot.MassArrayData	0.052	0.000	0.055
position	0.016	0.000	0.019
revComplement	0	0	0
rnaDigest	0.008	0.000	0.007
samples	0.036	0.000	0.038
sum.MassArraySpectrum	0.792	0.000	0.793