BioC 3.4: CHECK report for MassArray on moscato1

Package: MassArray

Version: 1.25.0

Command: rm -rf MassArray.buildbin-libdir MassArray.Rcheck && mkdir MassArray.buildbin-libdir MassArray.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MassArray.buildbin-libdir MassArray_1.25.0.tar.gz >MassArray.Rcheck\00install.out 2>&1 && cp MassArray.Rcheck\00install.out MassArray-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=MassArray.buildbin-libdir --install="check:MassArray-install.out" --force-multiarch --no-vignettes --timings MassArray_1.25.0.tar.gz

StartedAt: 2016-09-20 11:31:06 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 11:32:38 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 91.2 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 MassArray.Rcheck && mkdir MassArray.buildbin-libdir MassArray.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MassArray.buildbin-libdir MassArray_1.25.0.tar.gz >MassArray.Rcheck\00install.out 2>&1 && cp MassArray.Rcheck\00install.out MassArray-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=MassArray.buildbin-libdir --install="check:MassArray-install.out" --force-multiarch --no-vignettes --timings MassArray_1.25.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/MassArray.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-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 '1.25.0'
* 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'
$<-,MassArrayData: no visible global function definition for 'slot<-'
$<-,MassArrayFragment: no visible global function definition for
  'slot<-'
$<-,MassArrayPeak: no visible global function definition for 'slot<-'
$<-,MassArraySpectrum: no visible global function definition for
  'slot<-'
initialize,MassArrayData: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  read.table slot<-
Consider adding
  importFrom("methods", "slot<-")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
evaluateSNPs 16.02      0   16.02
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
evaluateSNPs 19.78   0.02    19.8
* 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
  'D:/biocbld/bbs-3.4-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_1.25.0.zip
* DONE (MassArray)

name	user	system	elapsed
MassArray.example.data	0.03	0.00	0.03
MassArrayData-class	0.00	0.02	0.01
MassArrayFragment-class	0	0	0
MassArrayPeak-class	0	0	0
MassArraySpectrum-class	0	0	0
ampliconPrediction	0.95	0.00	0.96
analyzeCpGs	0.06	0.01	0.07
bisConvert	0	0	0
calcMW	0	0	0
calcMeth	0	0	0
calcPercentAdduct	0.03	0.00	0.04
calcPercentConversion	0.02	0.00	0.01
combine	0.28	0.00	0.28
convControl	0.03	0.00	0.03
countCGs	0	0	0
createWiggle	0.02	0.00	0.02
estimatePrimerDimer	0.06	0.00	0.06
evaluateSNPs	16.02	0.00	16.02
expandSequence	0	0	0
findCollisions	0	0	0
findFragments	0.02	0.00	0.02
findPeaks	0	0	0
identifySNPs	0.02	0.00	0.02
inSilicoFragmentation	0	0	0
isAssayable	0	0	0
numCollisions	0	0	0
plot.MassArrayData	0.03	0.00	0.03
position	0	0	0
revComplement	0	0	0
rnaDigest	0	0	0
samples	0.02	0.00	0.02
sum.MassArraySpectrum	0.15	0.00	0.15

name	user	system	elapsed
MassArray.example.data	0.03	0.00	0.03
MassArrayData-class	0	0	0
MassArrayFragment-class	0.02	0.00	0.02
MassArrayPeak-class	0	0	0
MassArraySpectrum-class	0	0	0
ampliconPrediction	1.25	0.00	1.26
analyzeCpGs	0.11	0.00	0.11
bisConvert	0	0	0
calcMW	0	0	0
calcMeth	0.01	0.00	0.02
calcPercentAdduct	0.05	0.00	0.05
calcPercentConversion	0.03	0.00	0.03
combine	0.42	0.00	0.42
convControl	0.03	0.00	0.03
countCGs	0	0	0
createWiggle	0.02	0.00	0.01
estimatePrimerDimer	0.05	0.00	0.05
evaluateSNPs	19.78	0.02	19.80
expandSequence	0	0	0
findCollisions	0	0	0
findFragments	0.01	0.00	0.01
findPeaks	0	0	0
identifySNPs	0.02	0.00	0.02
inSilicoFragmentation	0	0	0
isAssayable	0	0	0
numCollisions	0	0	0
plot.MassArrayData	0.02	0.01	0.04
position	0.01	0.00	0.01
revComplement	0	0	0
rnaDigest	0.02	0.00	0.02
samples	0	0	0
sum.MassArraySpectrum	0.17	0.00	0.19