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BioC 3.3: CHECK report for RCytoscape on zin2

This page was generated on 2016-10-13 12:42:29 -0700 (Thu, 13 Oct 2016).

Package 947/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCytoscape 1.22.0
Paul Shannon
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/RCytoscape
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ TIMEOUT ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
oaxaca Mac OS X Mavericks (10.9.5) / x86_64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...

Summary

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

Command output

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


* 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 ...

RCytoscape.Rcheck/00install.out:

* 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)

RCytoscape.Rcheck/RCytoscape-Ex.timings:

nameusersystemelapsed
CytoscapeConnection0.0410.0040.073
CytoscapeConnectionClass-class0.0010.0000.001
CytoscapeWindow0.0480.0000.089
CytoscapeWindowClass-class0.1090.0000.160
addCyEdge0.3570.0053.690
addCyNode0.3600.0005.708
addGraphToGraph0.4680.0075.927
clearMsg0.0080.0000.014
clearSelection0.3160.0043.468
copyVisualStyle0.3360.0126.612
createWindowFromSelection1.7250.0445.881
cy2.edge.names0.0080.0000.008
deleteAllWindows0.2190.0121.373
deleteEdgeAttribute0.3120.0045.591
deleteNodeAttribute0.3140.0043.580
deleteSelectedEdges0.3300.0044.623
deleteSelectedNodes0.3770.0004.639
deleteWindow0.3530.0124.701
demoSimpleGraph0.4330.0047.693
displayGraph0.2880.0084.548
dockPanel0.0210.0000.035
eda0.0050.0040.006
eda.names0.0030.0000.005
existing.CytoscapeWindow1.5050.0205.093
fitContent0.3420.0043.727
fitSelectedContent0.3690.0123.671
floatPanel0.0210.0000.090
getAdjacentEdgeNames0.0080.0000.007
getAllEdgeAttributes0.3060.0123.617
getAllEdges0.2690.0123.409
getAllNodeAttributes0.3070.0044.579
getAllNodes0.2890.0084.430
getArrowShapes0.0100.0000.015
getAttributeClassNames0.0010.0000.001
getCenter0.3140.0005.572
getDefaultBackgroundColor0.0110.0000.016
getDefaultEdgeReverseSelectionColor0.0110.0000.016
getDefaultEdgeSelectionColor0.0110.0000.015
getDefaultNodeReverseSelectionColor0.0080.0000.016
getDefaultNodeSelectionColor0.0030.0080.016
getDirectlyModifiableVisualProperties0.0180.0000.022
getEdgeAttribute0.3280.0043.552
getEdgeAttributeNames0.0100.0000.014
getEdgeCount0.3110.0083.536
getFirstNeighbors0.3400.0004.572
getGraph0.2700.0003.385
getGraphFromCyWindow1.4850.0326.177
getLayoutNameMapping0.0160.0000.021
getLayoutNames0.0120.0000.016
getLayoutPropertyNames0.0130.0000.017
getLayoutPropertyType0.1250.0000.166
getLayoutPropertyValue0.1230.0050.168
getLineStyles0.0130.0000.017
getNodeAttribute0.3240.0114.550
getNodeAttributeNames0.0120.0000.016
getNodeCount0.2960.0045.519
getNodePosition0.2960.0003.511
getNodeShapes0.0110.0000.015
getNodeSize0.4950.0045.800
getSelectedEdgeCount0.3280.0124.576
getSelectedEdges0.2950.0133.525
getSelectedNodeCount0.3400.0005.575
getSelectedNodes0.3450.0083.614
getViewCoordinates0.3150.0004.590
getVisualStyleNames0.0100.0000.014
getWindowCount0.1480.0000.335
getWindowID0.3080.0045.460
getWindowList0.0480.0000.057
getZoom0.3080.0043.548
hideAllPanels0.2440.0040.537
hideNodes0.1490.0000.641
hidePanel0.0230.0000.031