Package: MassArray

Version: 1.34.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MassArray.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MassArray_1.34.1.tar.gz

StartedAt: 2019-04-16 01:08:00 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:08:39 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 38.7 seconds

RetCode: 0

Status:  OK

CheckDir: MassArray.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MassArray.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MassArray_1.34.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/MassArray.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.34.1’
* 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 ... 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'
$<-,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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
evaluateSNPs 12.808  0.012  12.844
* 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-3.8-bioc/meat/MassArray.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL MassArray
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘MassArray’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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	0.02	0.00	0.02
MassArrayData-class	0.000	0.000	0.002
MassArrayFragment-class	0.000	0.000	0.001
MassArrayPeak-class	0.000	0.000	0.001
MassArraySpectrum-class	0	0	0
ampliconPrediction	1.224	0.000	1.225
analyzeCpGs	0.108	0.000	0.107
bisConvert	0	0	0
calcMW	0.000	0.000	0.001
calcMeth	0.012	0.000	0.009
calcPercentAdduct	0.036	0.000	0.038
calcPercentConversion	0.040	0.000	0.036
combine	0.412	0.008	0.421
convControl	0.02	0.00	0.02
countCGs	0	0	0
createWiggle	0.012	0.000	0.012
estimatePrimerDimer	0.044	0.000	0.044
evaluateSNPs	12.808	0.012	12.844
expandSequence	0.000	0.000	0.001
findCollisions	0.000	0.000	0.001
findFragments	0.016	0.000	0.012
findPeaks	0	0	0
identifySNPs	0.012	0.000	0.012
inSilicoFragmentation	0.000	0.004	0.006
isAssayable	0	0	0
numCollisions	0	0	0
plot.MassArrayData	0.016	0.000	0.017
position	0.008	0.000	0.006
revComplement	0	0	0
rnaDigest	0.004	0.000	0.003
samples	0.004	0.000	0.005
sum.MassArraySpectrum	0.128	0.000	0.127