Package: MassArray

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MassArray_1.4.0.tar.gz

StartedAt: 2011-10-20 15:53:41 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 15:55:15 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 93.3 seconds

RetCode: 0

Status:  OK

CheckDir: MassArray.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/MassArray.Rcheck'
* using R version 2.13.2 (2011-09-30)
* 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 '1.4.0'
* checking package namespace 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 352Kb to 192Kb
  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 ...
** testing if installed package can be loaded

* DONE (MassArray)

name	user	system	elapsed
MassArray.example.data	0.023	0.003	0.027
MassArrayData-class	0.001	0.001	0.002
MassArrayFragment-class	0.001	0.001	0.001
MassArrayPeak-class	0.001	0.000	0.001
MassArraySpectrum-class	0.001	0.001	0.001
ampliconPrediction	3.064	0.017	3.099
analyzeCpGs	0.302	0.003	0.313
bisConvert	0.001	0.000	0.001
calcMW	0.002	0.000	0.002
calcMeth	0.020	0.001	0.022
calcPercentAdduct	0.099	0.002	0.104
calcPercentConversion	0.065	0.002	0.072
combine	5.623	0.029	5.696
convControl	0.039	0.003	0.041
countCGs	0	0	0
createWiggle	0.018	0.003	0.021
estimatePrimerDimer	0.122	0.005	0.127
evaluateSNPs	39.183	0.094	39.447
expandSequence	0.001	0.000	0.001
findCollisions	0.001	0.000	0.000
findFragments	0.024	0.002	0.028
findPeaks	0.001	0.000	0.001
identifySNPs	0.040	0.001	0.041
inSilicoFragmentation	0.014	0.001	0.016
isAssayable	0.001	0.001	0.000
numCollisions	0.001	0.000	0.000
plot.MassArrayData	0.059	0.002	0.061
position	0.023	0.002	0.025
revComplement	0	0	0
rnaDigest	0.011	0.002	0.014
samples	0.034	0.001	0.035
sum.MassArraySpectrum	0.864	0.005	0.895