Package: MassArray

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MassArray_1.11.0.tar.gz

StartedAt: 2013-03-25 03:26:16 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:27:46 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 89.5 seconds

RetCode: 0

Status:  OK

CheckDir: MassArray.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/MassArray.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.11.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'MassArray' can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... NOTE
calcMeth: warning in matrix(0, nr = 0, nc = N): partial argument match
  of 'nr' to 'nrow'
calcMeth: warning in matrix(0, nr = 0, nc = N): partial argument match
  of 'nc' to 'ncol'
calcMeth: warning in matrix(0, nr = num.SNRs, nc = N): partial argument
  match of 'nr' to 'nrow'
calcMeth: warning in matrix(0, nr = num.SNRs, nc = N): partial argument
  match of 'nc' to 'ncol'
calcMeth: warning in matrix(0, nr = num.missing, nc = N): partial
  argument match of 'nr' to 'nrow'
calcMeth: warning in matrix(0, nr = num.missing, nc = N): partial
  argument match of 'nc' to 'ncol'
calcMeth: warning in matrix(0, nr = length(na.coefs), nc = N): partial
  argument match of 'nr' to 'nrow'
calcMeth: warning in matrix(0, nr = length(na.coefs), nc = N): partial
  argument match of 'nc' to 'ncol'
calcMeth : optimizeCoefficients: warning in matrix(0, nr =
  num.fragments, nc = N): partial argument match of 'nr' to 'nrow'
calcMeth : optimizeCoefficients: warning in matrix(0, nr =
  num.fragments, nc = N): partial argument match of 'nc' to 'ncol'
calcMeth : optimizeCoefficients: warning in matrix(NA, nr =
  length(coefs) + 1, nc = length(coefs)): partial argument match of
  'nr' to 'nrow'
calcMeth : optimizeCoefficients: warning in matrix(NA, nr =
  length(coefs) + 1, nc = length(coefs)): partial argument match of
  'nc' to 'ncol'
* 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 installed files from 'inst/doc' ... OK
* checking examples ... [43s/43s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
evaluateSNPs 33.97  0.022  33.994
* 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-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
** help
*** installing help indices
** building package indices
** installing vignettes
   'MassArray.Rnw' 
** testing if installed package can be loaded
* DONE (MassArray)

name	user	system	elapsed
MassArray.example.data	0.037	0.011	0.049
MassArrayData-class	0.005	0.005	0.011
MassArrayFragment-class	0.005	0.005	0.009
MassArrayPeak-class	0.005	0.005	0.010
MassArraySpectrum-class	0.006	0.006	0.013
ampliconPrediction	2.178	0.016	2.195
analyzeCpGs	0.236	0.010	0.246
bisConvert	0.006	0.006	0.012
calcMW	0.008	0.005	0.012
calcMeth	0.029	0.011	0.039
calcPercentAdduct	0.105	0.010	0.115
calcPercentConversion	0.070	0.012	0.081
combine	3.558	0.020	3.579
convControl	0.036	0.009	0.045
countCGs	0.006	0.005	0.012
createWiggle	0.020	0.007	0.027
estimatePrimerDimer	0.072	0.008	0.079
evaluateSNPs	33.970	0.022	33.994
expandSequence	0.013	0.008	0.021
findCollisions	0.012	0.007	0.018
findFragments	0.037	0.011	0.048
findPeaks	0.008	0.007	0.016
identifySNPs	0.052	0.009	0.060
inSilicoFragmentation	0.021	0.008	0.030
isAssayable	0.009	0.009	0.018
numCollisions	0.008	0.007	0.015
plot.MassArrayData	0.046	0.008	0.055
position	0.039	0.010	0.050
revComplement	0.006	0.005	0.010
rnaDigest	0.011	0.007	0.020
samples	0.034	0.008	0.042
sum.MassArraySpectrum	0.544	0.009	0.553