BioC 3.3: CHECK report for RCytoscape on zin2

Package: RCytoscape

Version: 1.22.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings RCytoscape_1.22.0.tar.gz

StartedAt: 2016-10-13 05:50:10 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 06:30:11 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 2400.4 seconds

RetCode: None

Status:  TIMEOUT

CheckDir: RCytoscape.Rcheck

Warnings: NA

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings RCytoscape_1.22.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-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 ‘1.22.0’
* 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 ...

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

name	user	system	elapsed
CytoscapeConnection	0.041	0.004	0.073
CytoscapeConnectionClass-class	0.001	0.000	0.001
CytoscapeWindow	0.048	0.000	0.089
CytoscapeWindowClass-class	0.109	0.000	0.160
addCyEdge	0.357	0.005	3.690
addCyNode	0.360	0.000	5.708
addGraphToGraph	0.468	0.007	5.927
clearMsg	0.008	0.000	0.014
clearSelection	0.316	0.004	3.468
copyVisualStyle	0.336	0.012	6.612
createWindowFromSelection	1.725	0.044	5.881
cy2.edge.names	0.008	0.000	0.008
deleteAllWindows	0.219	0.012	1.373
deleteEdgeAttribute	0.312	0.004	5.591
deleteNodeAttribute	0.314	0.004	3.580
deleteSelectedEdges	0.330	0.004	4.623
deleteSelectedNodes	0.377	0.000	4.639
deleteWindow	0.353	0.012	4.701
demoSimpleGraph	0.433	0.004	7.693
displayGraph	0.288	0.008	4.548
dockPanel	0.021	0.000	0.035
eda	0.005	0.004	0.006
eda.names	0.003	0.000	0.005
existing.CytoscapeWindow	1.505	0.020	5.093
fitContent	0.342	0.004	3.727
fitSelectedContent	0.369	0.012	3.671
floatPanel	0.021	0.000	0.090
getAdjacentEdgeNames	0.008	0.000	0.007
getAllEdgeAttributes	0.306	0.012	3.617
getAllEdges	0.269	0.012	3.409
getAllNodeAttributes	0.307	0.004	4.579
getAllNodes	0.289	0.008	4.430
getArrowShapes	0.010	0.000	0.015
getAttributeClassNames	0.001	0.000	0.001
getCenter	0.314	0.000	5.572
getDefaultBackgroundColor	0.011	0.000	0.016
getDefaultEdgeReverseSelectionColor	0.011	0.000	0.016
getDefaultEdgeSelectionColor	0.011	0.000	0.015
getDefaultNodeReverseSelectionColor	0.008	0.000	0.016
getDefaultNodeSelectionColor	0.003	0.008	0.016
getDirectlyModifiableVisualProperties	0.018	0.000	0.022
getEdgeAttribute	0.328	0.004	3.552
getEdgeAttributeNames	0.010	0.000	0.014
getEdgeCount	0.311	0.008	3.536
getFirstNeighbors	0.340	0.000	4.572
getGraph	0.270	0.000	3.385
getGraphFromCyWindow	1.485	0.032	6.177
getLayoutNameMapping	0.016	0.000	0.021
getLayoutNames	0.012	0.000	0.016
getLayoutPropertyNames	0.013	0.000	0.017
getLayoutPropertyType	0.125	0.000	0.166
getLayoutPropertyValue	0.123	0.005	0.168
getLineStyles	0.013	0.000	0.017
getNodeAttribute	0.324	0.011	4.550
getNodeAttributeNames	0.012	0.000	0.016
getNodeCount	0.296	0.004	5.519
getNodePosition	0.296	0.000	3.511
getNodeShapes	0.011	0.000	0.015
getNodeSize	0.495	0.004	5.800
getSelectedEdgeCount	0.328	0.012	4.576
getSelectedEdges	0.295	0.013	3.525
getSelectedNodeCount	0.340	0.000	5.575
getSelectedNodes	0.345	0.008	3.614
getViewCoordinates	0.315	0.000	4.590
getVisualStyleNames	0.010	0.000	0.014
getWindowCount	0.148	0.000	0.335
getWindowID	0.308	0.004	5.460
getWindowList	0.048	0.000	0.057
getZoom	0.308	0.004	3.548
hideAllPanels	0.244	0.004	0.537
hideNodes	0.149	0.000	0.641
hidePanel	0.023	0.000	0.031