BioC 2.14: CHECK report for MassArray on moscato2

Package: MassArray

Version: 1.16.0

Command: rm -rf MassArray.buildbin-libdir && mkdir MassArray.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MassArray.buildbin-libdir MassArray_1.16.0.tar.gz >MassArray-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=MassArray.buildbin-libdir --install="check:MassArray-install.out" --force-multiarch --no-vignettes --timings MassArray_1.16.0.tar.gz

StartedAt: 2014-10-08 02:36:59 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 02:38:19 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 80.8 seconds

RetCode: 0

Status:  OK

CheckDir: MassArray.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf MassArray.buildbin-libdir && mkdir MassArray.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MassArray.buildbin-libdir MassArray_1.16.0.tar.gz >MassArray-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=MassArray.buildbin-libdir --install="check:MassArray-install.out" --force-multiarch --no-vignettes --timings MassArray_1.16.0.tar.gz
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/MassArray.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MassArray/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MassArray' version '1.16.0'
* 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 whether package 'MassArray' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... [19s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
evaluateSNPs 16.42      0   16.41
** running examples for arch 'x64' ... [25s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
evaluateSNPs 19.93      0   19.94
* 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 2 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/MassArray.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'MassArray' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MassArray' as MassArray_1.16.0.zip
* DONE (MassArray)

name	user	system	elapsed
MassArray.example.data	0.03	0.00	0.03
MassArrayData-class	0.00	0.01	0.01
MassArrayFragment-class	0	0	0
MassArrayPeak-class	0	0	0
MassArraySpectrum-class	0	0	0
ampliconPrediction	1.19	0.00	1.19
analyzeCpGs	0.12	0.00	0.12
bisConvert	0	0	0
calcMW	0	0	0
calcMeth	0.02	0.00	0.02
calcPercentAdduct	0.03	0.00	0.03
calcPercentConversion	0.03	0.00	0.03
combine	0.53	0.02	0.55
convControl	0.02	0.00	0.01
countCGs	0	0	0
createWiggle	0.01	0.00	0.02
estimatePrimerDimer	0.09	0.00	0.09
evaluateSNPs	16.42	0.00	16.41
expandSequence	0	0	0
findCollisions	0	0	0
findFragments	0.01	0.00	0.02
findPeaks	0	0	0
identifySNPs	0.02	0.00	0.01
inSilicoFragmentation	0	0	0
isAssayable	0	0	0
numCollisions	0	0	0
plot.MassArrayData	0.03	0.00	0.03
position	0.02	0.00	0.02
revComplement	0	0	0
rnaDigest	0	0	0
samples	0.02	0.00	0.01
sum.MassArraySpectrum	0.21	0.00	0.22

name	user	system	elapsed
MassArray.example.data	0.02	0.02	0.03
MassArrayData-class	0	0	0
MassArrayFragment-class	0	0	0
MassArrayPeak-class	0	0	0
MassArraySpectrum-class	0	0	0
ampliconPrediction	2.56	0.00	2.56
analyzeCpGs	0.22	0.00	0.22
bisConvert	0	0	0
calcMW	0.01	0.00	0.01
calcMeth	0.02	0.00	0.02
calcPercentAdduct	0.08	0.00	0.08
calcPercentConversion	0.05	0.00	0.04
combine	0.95	0.00	0.95
convControl	0.03	0.00	0.03
countCGs	0	0	0
createWiggle	0.01	0.00	0.02
estimatePrimerDimer	0.05	0.00	0.05
evaluateSNPs	19.93	0.00	19.94
expandSequence	0	0	0
findCollisions	0.02	0.00	0.02
findFragments	0	0	0
findPeaks	0	0	0
identifySNPs	0.01	0.00	0.02
inSilicoFragmentation	0.02	0.00	0.01
isAssayable	0	0	0
numCollisions	0	0	0
plot.MassArrayData	0.03	0.00	0.03
position	0.01	0.00	0.02
revComplement	0	0	0
rnaDigest	0	0	0
samples	0.00	0.01	0.02
sum.MassArraySpectrum	0.30	0.00	0.29