Package: MassArray

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MassArray_1.2.0.tar.gz

StartedAt: 2011-03-31 06:40:19 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 06:41:52 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 93.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MassArray.Rcheck

Warnings: 1

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/MassArray.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* 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 ‘1.2.0’
* checking package name space information ...Warning: unknown namespace directive: S3Method(plot, MassArrayData)
Warning: unknown namespace directive: S3Method(sum, MassArraySpectrum)
 OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘MassArray’ can be installed ... WARNING
Found the following significant warnings:
  Warning: unknown namespace directive: S3Method(plot, MassArrayData)
  Warning: unknown namespace directive: S3Method(sum, MassArraySpectrum)
  Warning: unknown namespace directive: S3Method(plot, MassArrayData)
  Warning: unknown namespace directive: S3Method(sum, MassArraySpectrum)
See ‘/Users/biocbuild/bbs-2.7-bioc/meat/MassArray.Rcheck/00install.out’ for details.
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  ‘/Users/biocbuild/bbs-2.7-bioc/meat/MassArray.Rcheck/00check.log’
for details

* installing *source* package ‘MassArray’ ...
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Warning: unknown namespace directive: S3Method(plot, MassArrayData)
Warning: unknown namespace directive: S3Method(sum, MassArraySpectrum)
** help
*** installing help indices
** building package indices ...
Warning: unknown namespace directive: S3Method(plot, MassArrayData)
Warning: unknown namespace directive: S3Method(sum, MassArraySpectrum)
** testing if installed package can be loaded

* DONE (MassArray)

name	user	system	elapsed
MassArray.example.data	0.019	0.003	0.022
MassArrayData-class	0.004	0.000	0.004
MassArrayFragment-class	0.003	0.000	0.004
MassArrayPeak-class	0.003	0.001	0.003
MassArraySpectrum-class	0.002	0.000	0.002
ampliconPrediction	3.232	0.023	3.309
analyzeCpGs	0.302	0.003	0.331
bisConvert	0.000	0.000	0.001
calcMW	0.003	0.001	0.003
calcMeth	0.019	0.002	0.020
calcPercentAdduct	0.090	0.002	0.093
calcPercentConversion	0.069	0.003	0.073
combine	6.243	0.039	6.469
convControl	0.087	0.003	0.092
countCGs	0.001	0.000	0.001
createWiggle	0.017	0.003	0.020
estimatePrimerDimer	0.099	0.005	0.104
evaluateSNPs	37.141	0.129	37.920
expandSequence	0.001	0.000	0.002
findCollisions	0.000	0.000	0.001
findFragments	0.025	0.002	0.028
findPeaks	0.001	0.000	0.001
identifySNPs	0.042	0.001	0.043
inSilicoFragmentation	0.016	0.002	0.017
isAssayable	0.000	0.000	0.001
numCollisions	0.001	0.000	0.001
plot.MassArrayData	0.059	0.002	0.061
position	0.028	0.002	0.030
revComplement	0.000	0.000	0.001
rnaDigest	0.009	0.002	0.012
samples	0.049	0.002	0.052
sum.MassArraySpectrum	0.860	0.006	0.870