BioC 3.0: CHECK report for MassArray on moscato1

Package: MassArray

Version: 1.18.0

Command: rm -rf MassArray.buildbin-libdir MassArray.Rcheck && mkdir MassArray.buildbin-libdir MassArray.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MassArray.buildbin-libdir MassArray_1.18.0.tar.gz >MassArray.Rcheck\00install.out 2>&1 && cp MassArray.Rcheck\00install.out MassArray-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=MassArray.buildbin-libdir --install="check:MassArray-install.out" --force-multiarch --no-vignettes --timings MassArray_1.18.0.tar.gz

StartedAt: 2015-04-10 02:45:36 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 02:47:06 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 90.1 seconds

RetCode: 0

Status:  OK

CheckDir: MassArray.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MassArray.buildbin-libdir MassArray.Rcheck && mkdir MassArray.buildbin-libdir MassArray.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MassArray.buildbin-libdir MassArray_1.18.0.tar.gz >MassArray.Rcheck\00install.out 2>&1 && cp MassArray.Rcheck\00install.out MassArray-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=MassArray.buildbin-libdir --install="check:MassArray-install.out" --force-multiarch --no-vignettes --timings MassArray_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/MassArray.Rcheck'
* using R version 3.1.3 (2015-03-09)
* 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 '1.18.0'
* 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' ... [21s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
evaluateSNPs 17.48      0   17.49
** running examples for arch 'x64' ... [25s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
evaluateSNPs 21.15   0.01   21.17
* 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-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_1.18.0.zip
* DONE (MassArray)

name	user	system	elapsed
MassArray.example.data	0.02	0.00	0.02
MassArrayData-class	0	0	0
MassArrayFragment-class	0	0	0
MassArrayPeak-class	0	0	0
MassArraySpectrum-class	0	0	0
ampliconPrediction	1.07	0.00	1.07
analyzeCpGs	0.14	0.00	0.53
bisConvert	0	0	0
calcMW	0	0	0
calcMeth	0	0	0
calcPercentAdduct	0.04	0.00	0.04
calcPercentConversion	0.04	0.00	0.04
combine	0.48	0.00	0.48
convControl	0.01	0.01	0.03
countCGs	0	0	0
createWiggle	0.00	0.02	0.02
estimatePrimerDimer	0.07	0.00	0.06
evaluateSNPs	17.48	0.00	17.49
expandSequence	0	0	0
findCollisions	0	0	0
findFragments	0.02	0.00	0.01
findPeaks	0	0	0
identifySNPs	0.03	0.00	0.03
inSilicoFragmentation	0	0	0
isAssayable	0	0	0
numCollisions	0	0	0
plot.MassArrayData	0.02	0.01	0.03
position	0.00	0.02	0.02
revComplement	0	0	0
rnaDigest	0.00	0.01	0.02
samples	0	0	0
sum.MassArraySpectrum	0.32	0.00	0.32

name	user	system	elapsed
MassArray.example.data	0.01	0.00	0.02
MassArrayData-class	0	0	0
MassArrayFragment-class	0	0	0
MassArrayPeak-class	0	0	0
MassArraySpectrum-class	0	0	0
ampliconPrediction	1.62	0.00	1.62
analyzeCpGs	0.25	0.00	0.25
bisConvert	0	0	0
calcMW	0	0	0
calcMeth	0	0	0
calcPercentAdduct	0.05	0.00	0.05
calcPercentConversion	0.03	0.00	0.03
combine	0.64	0.02	0.65
convControl	0.03	0.00	0.03
countCGs	0	0	0
createWiggle	0	0	0
estimatePrimerDimer	0.06	0.00	0.06
evaluateSNPs	21.15	0.01	21.17
expandSequence	0	0	0
findCollisions	0	0	0
findFragments	0.02	0.00	0.02
findPeaks	0	0	0
identifySNPs	0.03	0.00	0.03
inSilicoFragmentation	0.02	0.00	0.01
isAssayable	0	0	0
numCollisions	0	0	0
plot.MassArrayData	0.03	0.00	0.04
position	0.01	0.00	0.01
revComplement	0	0	0
rnaDigest	0	0	0
samples	0.02	0.00	0.02
sum.MassArraySpectrum	0.28	0.00	0.28