BioC 2.13: CHECK report for MassArray on perceval

Package: MassArray

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MassArray_1.14.0.tar.gz

StartedAt: 2014-04-05 02:26:36 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:27:59 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 82.8 seconds

RetCode: 0

Status:  OK

CheckDir: MassArray.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/MassArray.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-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 ‘1.14.0’
* 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 ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘MassArray.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [39s/40s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
evaluateSNPs 29.683   0.11  30.293
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	0.031	0.002	0.033
MassArrayData-class	0.007	0.001	0.007
MassArrayFragment-class	0.005	0.001	0.006
MassArrayPeak-class	0.005	0.000	0.005
MassArraySpectrum-class	0.005	0.000	0.006
ampliconPrediction	2.034	0.023	2.098
analyzeCpGs	0.261	0.008	0.273
bisConvert	0.005	0.000	0.005
calcMW	0.010	0.000	0.011
calcMeth	0.032	0.001	0.035
calcPercentAdduct	0.059	0.002	0.061
calcPercentConversion	0.049	0.002	0.055
combine	4.606	0.044	4.733
convControl	0.039	0.003	0.043
countCGs	0.005	0.000	0.005
createWiggle	0.018	0.002	0.020
estimatePrimerDimer	0.063	0.003	0.067
evaluateSNPs	29.683	0.110	30.293
expandSequence	0.027	0.001	0.030
findCollisions	0.009	0.001	0.009
findFragments	0.032	0.003	0.035
findPeaks	0.008	0.001	0.009
identifySNPs	0.038	0.000	0.040
inSilicoFragmentation	0.016	0.002	0.018
isAssayable	0.004	0.001	0.004
numCollisions	0.004	0.000	0.005
plot.MassArrayData	0.040	0.001	0.044
position	0.022	0.001	0.024
revComplement	0.004	0.000	0.005
rnaDigest	0.009	0.001	0.012
samples	0.041	0.001	0.043
sum.MassArraySpectrum	0.506	0.003	0.513