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BioC 3.4: CHECK report for BrowserViz on morelia

This page was generated on 2017-04-15 16:26:18 -0400 (Sat, 15 Apr 2017).

Package 143/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BrowserViz 1.6.0
Paul Shannon
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/BrowserViz
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: BrowserViz
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BrowserViz_1.6.0.tar.gz
StartedAt: 2017-04-14 23:22:38 -0700 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:39:52 -0700 (Fri, 14 Apr 2017)
EllapsedTime: 1034.0 seconds
RetCode: 1
Status:  ERROR 
CheckDir: BrowserViz.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BrowserViz_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/BrowserViz.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 ‘BrowserViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BrowserViz’ 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 ... 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 ... 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)
LSOpenURLsWithRole() failed with error -10810 for the URL http://localhost:4000.
Error: totalWait < maxWaitPermitted is not TRUE
Execution halted
* 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 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/BrowserViz.Rcheck/00check.log’
for details.

BrowserViz.Rcheck/00install.out:

* 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)

BrowserViz.Rcheck/BrowserViz-Ex.timings:

nameusersystemelapsed