BioC 2.12: CHECK report for MassArray on george2

Package: MassArray

Version: 1.12.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings MassArray_1.12.0.tar.gz

StartedAt: 2013-10-09 03:03:54 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:05:32 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 98.4 seconds

RetCode: 0

Status:  OK

CheckDir: MassArray.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/MassArray.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.12.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [50s/51s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
evaluateSNPs 36.431  0.036  37.000
combine       7.268  0.008   7.316
* 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
  ‘/home/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	0.036	0.004	0.040
MassArrayData-class	0.016	0.000	0.017
MassArrayFragment-class	0.008	0.000	0.010
MassArrayPeak-class	0.004	0.004	0.010
MassArraySpectrum-class	0.012	0.000	0.009
ampliconPrediction	2.812	0.016	2.828
analyzeCpGs	0.212	0.000	0.213
bisConvert	0.008	0.000	0.010
calcMW	0.012	0.000	0.014
calcMeth	0.036	0.000	0.035
calcPercentAdduct	0.084	0.000	0.086
calcPercentConversion	0.072	0.000	0.074
combine	7.268	0.008	7.316
convControl	0.080	0.000	0.081
countCGs	0.016	0.000	0.014
createWiggle	0.208	0.008	0.213
estimatePrimerDimer	0.112	0.000	0.112
evaluateSNPs	36.431	0.036	37.000
expandSequence	0.016	0.000	0.019
findCollisions	0.020	0.000	0.016
findFragments	0.040	0.000	0.039
findPeaks	0.012	0.000	0.011
identifySNPs	0.048	0.000	0.049
inSilicoFragmentation	0.020	0.000	0.023
isAssayable	0.012	0.000	0.010
numCollisions	0.008	0.000	0.007
plot.MassArrayData	0.048	0.004	0.050
position	0.040	0.000	0.039
revComplement	0.016	0.000	0.015
rnaDigest	0.016	0.000	0.019
samples	0.068	0.000	0.066
sum.MassArraySpectrum	0.852	0.000	0.852