BioC 3.2: CHECK report for MassArray on linux1.bioconductor.org

Package: MassArray

Version: 1.22.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MassArray_1.22.0.tar.gz

StartedAt: 2015-10-27 05:18:31 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:19:12 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 40.3 seconds

RetCode: 0

Status:  OK

CheckDir: MassArray.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MassArray_1.22.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/MassArray.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.22.0’
* 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 ... [1s/1s] 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/19s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
evaluateSNPs 16.135      0  16.152
* 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
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-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	0.019	0.004	0.023
MassArrayData-class	0.000	0.003	0.002
MassArrayFragment-class	0.001	0.001	0.002
MassArrayPeak-class	0.001	0.000	0.002
MassArraySpectrum-class	0.000	0.003	0.001
ampliconPrediction	1.380	0.017	1.398
analyzeCpGs	0.124	0.000	0.124
bisConvert	0.001	0.000	0.001
calcMW	0.002	0.000	0.002
calcMeth	0.012	0.000	0.012
calcPercentAdduct	0.047	0.000	0.047
calcPercentConversion	0.018	0.003	0.022
combine	0.596	0.001	0.595
convControl	0.015	0.003	0.019
countCGs	0.000	0.000	0.001
createWiggle	0.004	0.001	0.007
estimatePrimerDimer	0.037	0.000	0.038
evaluateSNPs	16.135	0.000	16.152
expandSequence	0.001	0.000	0.001
findCollisions	0.000	0.000	0.001
findFragments	0.006	0.000	0.007
findPeaks	0.001	0.000	0.000
identifySNPs	0.009	0.003	0.013
inSilicoFragmentation	0.006	0.000	0.006
isAssayable	0.000	0.000	0.001
numCollisions	0	0	0
plot.MassArrayData	0.015	0.004	0.018
position	0.006	0.000	0.006
revComplement	0.001	0.000	0.001
rnaDigest	0.005	0.000	0.005
samples	0.008	0.000	0.008
sum.MassArraySpectrum	0.144	0.000	0.145