Package: MassArray

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MassArray_1.5.0.tar.gz

StartedAt: 2011-07-07 04:16:05 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 04:17:39 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 94.1 seconds

RetCode: 0

Status:  OK

CheckDir: MassArray.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/MassArray.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 '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 sizes of PDF files under 'inst/doc' ... 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	0.026	0.003	0.030
MassArrayData-class	0.001	0.000	0.002
MassArrayFragment-class	0.001	0.001	0.001
MassArrayPeak-class	0.001	0.001	0.001
MassArraySpectrum-class	0.000	0.000	0.001
ampliconPrediction	3.248	0.021	3.301
analyzeCpGs	0.318	0.004	0.324
bisConvert	0.000	0.000	0.001
calcMW	0.002	0.001	0.002
calcMeth	0.019	0.002	0.021
calcPercentAdduct	0.096	0.003	0.100
calcPercentConversion	0.072	0.002	0.074
combine	5.741	0.044	5.811
convControl	0.039	0.003	0.043
countCGs	0.000	0.000	0.001
createWiggle	0.024	0.004	0.029
estimatePrimerDimer	0.114	0.004	0.119
evaluateSNPs	38.231	0.129	38.642
expandSequence	0.002	0.000	0.002
findCollisions	0	0	0
findFragments	0.025	0.002	0.027
findPeaks	0.000	0.000	0.001
identifySNPs	0.040	0.001	0.041
inSilicoFragmentation	0.015	0.002	0.017
isAssayable	0	0	0
numCollisions	0.000	0.001	0.001
plot.MassArrayData	0.055	0.002	0.057
position	0.026	0.002	0.027
revComplement	0	0	0
rnaDigest	0.009	0.001	0.011
samples	0.040	0.003	0.043
sum.MassArraySpectrum	0.828	0.004	0.844