BioC 3.4: CHECK report for GreyListChIP on morelia

Package: GreyListChIP

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GreyListChIP_1.6.0.tar.gz

StartedAt: 2017-04-15 03:17:24 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 03:20:47 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 202.2 seconds

RetCode: 0

Status:  OK

CheckDir: GreyListChIP.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GreyListChIP_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/GreyListChIP.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GreyListChIP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GreyListChIP’ version ‘1.6.0’
* 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 ‘GreyListChIP’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 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
calcThreshold.GreyList: no visible global function definition for
  ‘qnbinom’
export.GreyList: no visible global function definition for
  ‘write.table’
initialize.GreyList: no visible global function definition for
  ‘callNextMethod’
loadKaryotype.GreyList: no visible global function definition for
  ‘read.table’
calcThreshold,GreyList: no visible global function definition for
  ‘qnbinom’
export,GreyList-character-missing: no visible global function
  definition for ‘write.table’
initialize,GreyList: no visible global function definition for
  ‘callNextMethod’
loadKaryotype,GreyList: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  callNextMethod qnbinom read.table write.table
Consider adding
  importFrom("methods", "callNextMethod")
  importFrom("stats", "qnbinom")
  importFrom("utils", "read.table", "write.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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/GreyListChIP.Rcheck/00check.log’
for details.

* installing *source* package ‘GreyListChIP’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GreyListChIP)

name	user	system	elapsed
GreyList-class	0.641	0.022	0.921
calcThreshold-methods	0.229	0.011	0.339
countReads-methods	0.029	0.005	0.045
getKaryotype-methods	0.158	0.014	2.193
greyListBS	0.117	0.005	0.122
loadKaryotype-methods	0.267	0.025	0.405
makeGreyList-methods	0.067	0.008	0.081