BioC 3.2: CHECK report for RCytoscape on zin1

Package: RCytoscape

Version: 1.20.1

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RCytoscape_1.20.1.tar.gz

StartedAt: 2016-04-23 04:28:35 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 05:08:35 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 2400.3 seconds

RetCode: None

Status:  TIMEOUT

CheckDir: RCytoscape.Rcheck

Warnings: NA

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RCytoscape_1.20.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/RCytoscape.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.20.1’
* 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 ... [4s/4s] 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'
.multiGraphToNodePairTable: no visible global function definition for
  ‘edgeSets’
makeRandomGraph: no visible global function definition for
  ‘randomGraph’
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’
* 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	0.033	0.003	0.226
CytoscapeConnectionClass-class	0.001	0.000	0.001
CytoscapeWindow	0.036	0.003	0.096
CytoscapeWindowClass-class	0.055	0.001	0.105
addCyEdge	0.362	0.008	4.757
addCyNode	0.314	0.008	3.620
addGraphToGraph	0.479	0.008	6.907
clearMsg	0.005	0.004	0.014
clearSelection	0.320	0.008	5.474
copyVisualStyle	0.352	0.004	4.619
createWindowFromSelection	1.720	0.023	7.783
cy2.edge.names	0.007	0.001	0.008
deleteAllWindows	0.222	0.012	1.386
deleteEdgeAttribute	0.322	0.008	4.606
deleteNodeAttribute	0.383	0.008	5.640
deleteSelectedEdges	0.347	0.000	3.611
deleteSelectedNodes	0.365	0.004	6.623
deleteWindow	0.412	0.000	4.703
demoSimpleGraph	0.431	0.008	6.688
displayGraph	0.290	0.004	4.551
dockPanel	0.021	0.000	0.035
eda	0.007	0.000	0.007
eda.names	0.006	0.000	0.006
existing.CytoscapeWindow	1.497	0.048	5.141
fitContent	0.372	0.004	5.721
fitSelectedContent	0.375	0.004	3.685
floatPanel	0.023	0.000	0.105
getAdjacentEdgeNames	0.006	0.000	0.007
getAllEdgeAttributes	0.307	0.000	3.603
getAllEdges	0.282	0.004	4.417
getAllNodeAttributes	0.282	0.012	3.544
getAllNodes	0.289	0.000	5.415
getArrowShapes	0.009	0.000	0.014
getAttributeClassNames	0.001	0.000	0.000
getCenter	0.300	0.009	3.553
getDefaultBackgroundColor	0.011	0.000	0.016
getDefaultEdgeReverseSelectionColor	0.011	0.000	0.015
getDefaultEdgeSelectionColor	0.011	0.000	0.016
getDefaultNodeReverseSelectionColor	0.011	0.000	0.015
getDefaultNodeSelectionColor	0.011	0.000	0.016
getDirectlyModifiableVisualProperties	0.018	0.000	0.022
getEdgeAttribute	0.324	0.004	4.539
getEdgeAttributeNames	0.009	0.000	0.014
getEdgeCount	0.304	0.000	3.510
getFirstNeighbors	0.337	0.012	4.581
getGraph	0.265	0.004	3.392
getGraphFromCyWindow	1.380	0.036	7.084
getLayoutNameMapping	0.014	0.000	0.020
getLayoutNames	0.012	0.000	0.016
getLayoutPropertyNames	0.011	0.000	0.017
getLayoutPropertyType	0.103	0.003	0.148
getLayoutPropertyValue	0.106	0.001	0.146
getLineStyles	0.010	0.000	0.015
getNodeAttribute	0.296	0.008	3.519
getNodeAttributeNames	0.012	0.000	0.016
getNodeCount	0.290	0.004	6.507
getNodePosition	0.294	0.004	4.516
getNodeShapes	0.010	0.000	0.015
getNodeSize	0.490	0.003	5.791
getSelectedEdgeCount	0.335	0.004	6.567
getSelectedEdges	0.311	0.004	3.538
getSelectedNodeCount	0.345	0.004	5.593
getSelectedNodes	0.357	0.012	5.622
getViewCoordinates	0.309	0.004	3.573
getVisualStyleNames	0.010	0.000	0.014
getWindowCount	0.152	0.000	0.343
getWindowID	0.322	0.000	4.466
getWindowList	0.047	0.000	0.057
getZoom	0.311	0.004	3.551
hideAllPanels	0.249	0.003	0.542
hideNodes	0.145	0.001	0.616
hidePanel	0.02	0.00	0.03