BioC 3.4: CHECK report for RCytoscape on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RCytoscape_1.23.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/RCytoscape.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 ‘RCytoscape/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCytoscape’ version ‘1.23.0’
* 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 ‘RCytoscape’ 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:
  ‘XMLRPC’
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 ... NOTE
Namespace in Imports field not imported from: ‘BiocGenerics’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addGraphToGraph,CytoscapeWindowClass: warning in
  .sendNodeAttributesForGraph(obj, other.graph, attr = attribute.name):
  partial argument match of 'attr' to 'attribute.name'
addGraphToGraph,CytoscapeWindowClass: warning in
  .sendEdgeAttributesForGraph(obj, other.graph, attr = attribute.name):
  partial argument match of 'attr' to 'attribute.name'
.BBSOverride: no visible global function definition for ‘as’
.multiGraphToNodePairTable: no visible global function definition for
  ‘edgeSets’
is.classic.graph: no visible global function definition for ‘is’
is.multiGraph: no visible global function definition for ‘is’
makeRandomGraph: no visible global function definition for
  ‘randomGraph’
valid.graph: no visible global function definition for ‘slotNames’
valid.graph: no visible global function definition for ‘is’
valid.title: no visible global function definition for ‘slotNames’
valid.uri: no visible global function definition for ‘slotNames’
valid.window.id: no visible global function definition for ‘slotNames’
validCyWin: no visible global function definition for ‘is’
restoreLayout,CytoscapeWindowClass: no visible binding for global
  variable ‘custom.layout’
restoreLayout,CytoscapeWindowClass : <anonymous>: no visible binding
  for global variable ‘custom.layout’
setEdgeAttributesDirect,CytoscapeWindowClass: no visible binding for
  '<<-' assignment to ‘timing.info’
setEdgeAttributesDirect,CytoscapeWindowClass: no visible binding for
  global variable ‘timing.info’
Undefined global functions or variables:
  as custom.layout edgeSets is randomGraph slotNames timing.info
Consider adding
  importFrom("methods", "as", "is", "slotNames")
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 ‘RCytoscape-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CytoscapeConnection
> ### Title: CytoscapeConnection
> ### Aliases: CytoscapeConnection
> ### Keywords: graph
> 
> ### ** Examples
> 
>   cy <- CytoscapeConnection ()
>   deleteAllWindows (cy)
Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to taipan port 8023: Connection refused
Calls: deleteAllWindows ... postForm -> .postForm -> .Call -> <Anonymous> -> fun
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘RCytoscape_unit_tests.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, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/RCytoscape.Rcheck/00check.log’
for details.
BioC 3.4: CHECK report for RCytoscape on zin1

Summary

Command output
