BioC 2.12: CHECK report for MassArray on petty

Package: MassArray

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MassArray_1.12.0.tar.gz

StartedAt: 2013-10-08 22:59:45 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:01:35 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 109.3 seconds

RetCode: 0

Status:  OK

CheckDir: MassArray.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/MassArray.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'MassArray/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MassArray' version '1.12.0'
* 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 ... [57s/58s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
evaluateSNPs 44.466  0.143  45.029
combine       6.169  0.040   6.243
* 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
** testing if installed package can be loaded
* DONE (MassArray)

name	user	system	elapsed
MassArray.example.data	0.040	0.003	0.044
MassArrayData-class	0.009	0.001	0.009
MassArrayFragment-class	0.006	0.001	0.006
MassArrayPeak-class	0.005	0.001	0.005
MassArraySpectrum-class	0.005	0.001	0.005
ampliconPrediction	3.158	0.030	3.196
analyzeCpGs	0.247	0.002	0.250
bisConvert	0.005	0.000	0.005
calcMW	0.010	0.001	0.010
calcMeth	0.033	0.001	0.034
calcPercentAdduct	0.096	0.003	0.099
calcPercentConversion	0.071	0.002	0.074
combine	6.169	0.040	6.243
convControl	0.146	0.004	0.153
countCGs	0.005	0.001	0.005
createWiggle	0.024	0.002	0.027
estimatePrimerDimer	0.112	0.002	0.116
evaluateSNPs	44.466	0.143	45.029
expandSequence	0.087	0.001	0.088
findCollisions	0.006	0.001	0.007
findFragments	0.028	0.002	0.030
findPeaks	0.008	0.000	0.009
identifySNPs	0.049	0.001	0.049
inSilicoFragmentation	0.021	0.002	0.022
isAssayable	0.012	0.000	0.013
numCollisions	0.006	0.000	0.007
plot.MassArrayData	0.056	0.001	0.058
position	0.036	0.001	0.043
revComplement	0.007	0.000	0.007
rnaDigest	0.015	0.001	0.017
samples	0.055	0.001	0.063
sum.MassArraySpectrum	0.901	0.016	0.920