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BioC 2.13: CHECK report for MassArray on zin1

This page was generated on 2014-04-05 09:47:51 -0700 (Sat, 05 Apr 2014).

Package 422/750HostnameOS / ArchBUILDCHECKBUILD BIN
MassArray 1.14.0
Reid F. Thompson
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/MassArray
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: MassArray
Version: 1.14.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings MassArray_1.14.0.tar.gz
StartedAt: 2014-04-05 02:16:23 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:17:12 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 48.9 seconds
RetCode: 0
Status:  OK 
CheckDir: MassArray.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/MassArray.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.14.0’
* 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 ... [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 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 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 ... [25s/25s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
evaluateSNPs 19.365  0.012  19.405
* 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
  ‘/home/biocbuild/bbs-2.13-bioc/meat/MassArray.Rcheck/00check.log’
for details.

MassArray.Rcheck/00install.out:

* 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)

MassArray.Rcheck/MassArray-Ex.timings:

nameusersystemelapsed
MassArray.example.data0.0200.0000.021
MassArrayData-class0.0040.0000.004
MassArrayFragment-class0.0040.0000.004
MassArrayPeak-class0.0040.0000.003
MassArraySpectrum-class0.0000.0040.003
ampliconPrediction1.4320.0041.445
analyzeCpGs0.1240.0000.124
bisConvert0.0040.0000.004
calcMW0.0040.0040.005
calcMeth0.0120.0080.019
calcPercentAdduct0.0440.0000.043
calcPercentConversion0.0720.0000.072
combine2.4000.0002.401
convControl0.0200.0040.026
countCGs0.0040.0000.004
createWiggle0.0120.0000.013
estimatePrimerDimer0.0600.0000.058
evaluateSNPs19.365 0.01219.405
expandSequence0.0040.0000.007
findCollisions0.0000.0000.003
findFragments0.0120.0040.015
findPeaks0.0040.0000.003
identifySNPs0.0560.0000.056
inSilicoFragmentation0.0080.0000.011
isAssayable0.0040.0000.003
numCollisions0.0000.0000.002
plot.MassArrayData0.0280.0000.030
position0.0160.0000.014
revComplement0.0000.0000.002
rnaDigest0.0080.0000.008
samples0.0200.0040.024
sum.MassArraySpectrum0.3760.0000.378