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: 2011-07-07 01:19:32 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 01:20:36 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 64.2 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) (2011-06-15 r56138)
* 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	0.016	0.004	0.019
MassArrayData-class	0.004	0.000	0.002
MassArrayFragment-class	0.000	0.000	0.002
MassArrayPeak-class	0.000	0.000	0.001
MassArraySpectrum-class	0.004	0.000	0.001
ampliconPrediction	2.532	0.008	2.544
analyzeCpGs	0.232	0.000	0.231
bisConvert	0	0	0
calcMW	0.004	0.000	0.001
calcMeth	0.012	0.000	0.014
calcPercentAdduct	0.064	0.000	0.065
calcPercentConversion	0.052	0.000	0.052
combine	5.976	0.028	6.107
convControl	0.028	0.004	0.031
countCGs	0	0	0
createWiggle	0.008	0.004	0.013
estimatePrimerDimer	0.072	0.004	0.083
evaluateSNPs	26.286	0.044	27.166
expandSequence	0.000	0.000	0.001
findCollisions	0.004	0.000	0.001
findFragments	0.008	0.000	0.015
findPeaks	0	0	0
identifySNPs	0.024	0.000	0.023
inSilicoFragmentation	0.008	0.000	0.010
isAssayable	0	0	0
numCollisions	0.000	0.000	0.001
plot.MassArrayData	0.032	0.000	0.034
position	0.016	0.000	0.017
revComplement	0	0	0
rnaDigest	0.008	0.004	0.010
samples	0.024	0.000	0.023
sum.MassArraySpectrum	0.608	0.000	0.607