BioC 3.3: CHECK report for BrowserViz on morelia

Package: BrowserViz

Version: 1.3.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BrowserViz_1.3.3.tar.gz

StartedAt: 2016-04-04 23:42:50 -0700 (Mon, 04 Apr 2016)

EndedAt: 2016-04-05 00:22:50 -0700 (Tue, 05 Apr 2016)

EllapsedTime: 2400.4 seconds

RetCode: None

Status:  TIMEOUT

CheckDir: BrowserViz.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BrowserViz_1.3.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/BrowserViz.Rcheck’
* using R version 3.3.0 beta (2016-03-30 r70404)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BrowserViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BrowserViz’ version ‘1.3.3’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BrowserViz’ can be installed ... [2s/2s] 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 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
.setupWebSocketHandlers : <anonymous> : <anonymous>: no visible global
  function definition for ‘is’
BrowserViz: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL is
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "browseURL")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘BrowserViz-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BrowserVizClass
> ### Title: BrowserViz: a base class (for extension) and standalone example
> ###   of R/Javascript interactive web browser visualization
> ### Aliases: BrowserViz class:BrowserVizClass BrowserVizClass-class
> ###   show,BrowserVizClass-method setBrowserWindowTitle
> ###   setBrowserWindowTitle,BrowserVizClass-method
> ###   \S4method{setBrowserWindowTitle}{BrowserVizClass}
> ###   getBrowserWindowSize getBrowserWindowSize,BrowserVizClass-method
> ###   \S4method{getBrowserWindowSize}{BrowserVizClass}
> ###   getBrowserWindowTitle getBrowserWindowTitle,BrowserVizClass-method
> ###   \S4method{getBrowserWindowTitle}{BrowserVizClass}
> ###   browserResponseReady browserResponseReady,BrowserVizClass-method
> ###   \S4method{browserResponseReady}{BrowserVizClass} getBrowserResponse
> ###   getBrowserResponse,BrowserVizClass-method
> ###   \S4method{getBrowserResponse}{BrowserVizClass} port
> ###   port,BrowserVizClass-method \S4method{port}{BrowserVizClass}
> ###   closeWebSocket closeWebSocket,BrowserVizClass-method
> ###   \S4method{closeWebSocket}{BrowserVizClass} getBrowserInfo
> ###   getBrowserInfo,BrowserVizClass-method
> ###   \S4method{getBrowserInfo}{BrowserVizClass} send
> ###   send,BrowserVizClass-method \S4method{send}{BrowserVizClass} ready
> ###   ready,BrowserVizClass-method \S4method{ready}{BrowserVizClass} toJSON
> ###   addRMessageHandler
> ### Keywords: classes methods
> 
> ### ** Examples
> 
>   library(BrowserViz)
>     
>   bv <- BrowserViz(4000:4024)
sh: phantomjs: command not found
Error: totalWait < maxWaitPermitted is not TRUE
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’

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

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