BioC 3.4: CHECK report for GreyListChIP on zin1

Package: GreyListChIP

Version: 1.5.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GreyListChIP_1.5.0.tar.gz

StartedAt: 2016-09-20 07:36:56 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 07:39:27 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 150.8 seconds

RetCode: 0

Status:  OK

CheckDir: GreyListChIP.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GreyListChIP_1.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/GreyListChIP.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.5.0’
* 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’
countReads.GreyList: no visible global function definition for ‘assays’
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’
countReads,GreyList: no visible global function definition for ‘assays’
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:
  assays 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
  ‘/home/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	0.548	0.004	0.551
calcThreshold-methods	0.496	0.000	0.680
countReads-methods	0.024	0.000	0.025
getKaryotype-methods	0.096	0.004	0.101
greyListBS	0.060	0.000	0.059
loadKaryotype-methods	0.476	0.004	0.499
makeGreyList-methods	0.044	0.004	0.096