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: 2011-05-09 15:34:53 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 15:36:24 -0700 (Mon, 09 May 2011)

EllapsedTime: 90.7 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) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-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 sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘MassArray.pdf’ from 347Kb to 162Kb
  consider running tools::compactPDF() on these files
* 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	0.025	0.003	0.028
MassArrayData-class	0.003	0.001	0.004
MassArrayFragment-class	0.003	0.001	0.004
MassArrayPeak-class	0.002	0.001	0.003
MassArraySpectrum-class	0.002	0.000	0.003
ampliconPrediction	3.220	0.017	3.248
analyzeCpGs	0.303	0.003	0.306
bisConvert	0.000	0.000	0.001
calcMW	0.003	0.000	0.003
calcMeth	0.022	0.002	0.024
calcPercentAdduct	0.093	0.002	0.095
calcPercentConversion	0.066	0.002	0.070
combine	5.785	0.028	5.826
convControl	0.042	0.003	0.047
countCGs	0	0	0
createWiggle	0.030	0.003	0.033
estimatePrimerDimer	0.104	0.003	0.107
evaluateSNPs	36.717	0.079	36.908
expandSequence	0.002	0.000	0.002
findCollisions	0.001	0.000	0.001
findFragments	0.024	0.002	0.026
findPeaks	0.000	0.000	0.001
identifySNPs	0.036	0.001	0.038
inSilicoFragmentation	0.014	0.001	0.016
isAssayable	0.000	0.000	0.001
numCollisions	0.001	0.000	0.001
plot.MassArrayData	0.056	0.002	0.059
position	0.022	0.002	0.024
revComplement	0.001	0.001	0.001
rnaDigest	0.009	0.001	0.011
samples	0.038	0.002	0.040
sum.MassArraySpectrum	0.791	0.003	0.797