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This page was generated on 2017-04-15 16:10:10 -0400 (Sat, 15 Apr 2017).
| Package 1017/1296 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| RCytoscape 1.24.1 Paul Shannon
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] |  | |||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... | |||||||||
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... | |||||||||
| Package: RCytoscape |
| Version: 1.24.1 |
| Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RCytoscape_1.24.1.tar.gz |
| StartedAt: 2017-04-15 00:47:23 -0400 (Sat, 15 Apr 2017) |
| EndedAt: 2017-04-15 00:48:11 -0400 (Sat, 15 Apr 2017) |
| EllapsedTime: 47.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RCytoscape.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RCytoscape_1.24.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/RCytoscape.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.24.1’
* 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/RCytoscape.Rcheck/00check.log’
for details.
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:
| name | user | system | elapsed | |
| CytoscapeConnection | 0.000 | 0.004 | 0.001 | |
| CytoscapeConnectionClass-class | 0.000 | 0.000 | 0.001 | |
| CytoscapeWindow | 0 | 0 | 0 | |
| CytoscapeWindowClass-class | 0 | 0 | 0 | |
| addCyEdge | 0 | 0 | 0 | |
| addCyNode | 0 | 0 | 0 | |
| addGraphToGraph | 0 | 0 | 0 | |
| clearMsg | 0 | 0 | 0 | |
| clearSelection | 0 | 0 | 0 | |
| copyVisualStyle | 0 | 0 | 0 | |
| createWindowFromSelection | 0 | 0 | 0 | |
| cy2.edge.names | 0.004 | 0.000 | 0.000 | |
| deleteAllWindows | 0.000 | 0.000 | 0.001 | |
| deleteEdgeAttribute | 0.000 | 0.000 | 0.001 | |
| deleteNodeAttribute | 0.004 | 0.000 | 0.001 | |
| deleteSelectedEdges | 0.000 | 0.000 | 0.001 | |
| deleteSelectedNodes | 0.000 | 0.000 | 0.001 | |
| deleteWindow | 0.000 | 0.000 | 0.001 | |
| demoSimpleGraph | 0.000 | 0.000 | 0.001 | |
| displayGraph | 0 | 0 | 0 | |
| dockPanel | 0 | 0 | 0 | |
| eda | 0.000 | 0.000 | 0.001 | |
| eda.names | 0.000 | 0.004 | 0.001 | |
| existing.CytoscapeWindow | 0 | 0 | 0 | |
| fitContent | 0 | 0 | 0 | |
| fitSelectedContent | 0 | 0 | 0 | |
| floatPanel | 0 | 0 | 0 | |
| getAdjacentEdgeNames | 0 | 0 | 0 | |
| getAllEdgeAttributes | 0 | 0 | 0 | |
| getAllEdges | 0 | 0 | 0 | |
| getAllNodeAttributes | 0.000 | 0.004 | 0.000 | |
| getAllNodes | 0.000 | 0.000 | 0.001 | |
| getArrowShapes | 0.000 | 0.000 | 0.001 | |
| getAttributeClassNames | 0.000 | 0.000 | 0.001 | |
| getCenter | 0.000 | 0.000 | 0.001 | |
| getDefaultBackgroundColor | 0 | 0 | 0 | |
| getDefaultEdgeReverseSelectionColor | 0 | 0 | 0 | |
| getDefaultEdgeSelectionColor | 0 | 0 | 0 | |
| getDefaultNodeReverseSelectionColor | 0 | 0 | 0 | |
| getDefaultNodeSelectionColor | 0 | 0 | 0 | |
| getDirectlyModifiableVisualProperties | 0 | 0 | 0 | |
| getEdgeAttribute | 0 | 0 | 0 | |
| getEdgeAttributeNames | 0.004 | 0.000 | 0.001 | |
| getEdgeCount | 0.000 | 0.000 | 0.001 | |
| getFirstNeighbors | 0.000 | 0.000 | 0.001 | |
| getGraph | 0.000 | 0.000 | 0.001 | |
| getGraphFromCyWindow | 0 | 0 | 0 | |
| getLayoutNameMapping | 0 | 0 | 0 | |
| getLayoutNames | 0 | 0 | 0 | |
| getLayoutPropertyNames | 0 | 0 | 0 | |
| getLayoutPropertyType | 0.004 | 0.000 | 0.001 | |
| getLayoutPropertyValue | 0.000 | 0.000 | 0.001 | |
| getLineStyles | 0.000 | 0.000 | 0.001 | |
| getNodeAttribute | 0.000 | 0.000 | 0.001 | |
| getNodeAttributeNames | 0 | 0 | 0 | |
| getNodeCount | 0 | 0 | 0 | |
| getNodePosition | 0 | 0 | 0 | |
| getNodeShapes | 0 | 0 | 0 | |
| getNodeSize | 0 | 0 | 0 | |
| getSelectedEdgeCount | 0.000 | 0.000 | 0.001 | |
| getSelectedEdges | 0 | 0 | 0 | |
| getSelectedNodeCount | 0.000 | 0.000 | 0.001 | |
| getSelectedNodes | 0.004 | 0.000 | 0.001 | |
| getViewCoordinates | 0.000 | 0.000 | 0.001 | |
| getVisualStyleNames | 0.000 | 0.000 | 0.001 | |
| getWindowCount | 0.000 | 0.000 | 0.001 | |
| getWindowID | 0 | 0 | 0 | |
| getWindowList | 0 | 0 | 0 | |
| getZoom | 0 | 0 | 0 | |
| hideAllPanels | 0 | 0 | 0 | |
| hideNodes | 0 | 0 | 0 | |
| hidePanel | 0.000 | 0.000 | 0.001 | |
| hideSelectedEdges | 0.000 | 0.000 | 0.001 | |
| hideSelectedNodes | 0.000 | 0.000 | 0.001 | |
| initEdgeAttribute | 0.000 | 0.000 | 0.001 | |
| initNodeAttribute | 0 | 0 | 0 | |
| invertEdgeSelection | 0 | 0 | 0 | |
| invertNodeSelection | 0 | 0 | 0 | |
| layoutNetwork | 0 | 0 | 0 | |
| lockNodeDimensions | 0 | 0 | 0 | |
| makeRandomGraph | 0 | 0 | 0 | |
| makeSimpleGraph | 0 | 0 | 0 | |
| msg | 0 | 0 | 0 | |
| new.CytoscapeWindow | 0.000 | 0.000 | 0.001 | |
| noa | 0.000 | 0.000 | 0.001 | |
| noa.names | 0.000 | 0.000 | 0.001 | |
| ping | 0.000 | 0.000 | 0.001 | |
| pluginVersion | 0.000 | 0.000 | 0.001 | |
| predictTimeToDisplayGraph | 0 | 0 | 0 | |
| raiseWindow | 0.000 | 0.000 | 0.001 | |
| redraw | 0.004 | 0.000 | 0.001 | |
| restoreLayout | 0.000 | 0.000 | 0.001 | |
| saveImage | 0.000 | 0.000 | 0.001 | |
| saveLayout | 0.000 | 0.000 | 0.001 | |
| saveNetwork | 0 | 0 | 0 | |
| selectEdges | 0 | 0 | 0 | |
| selectFirstNeighborsOfSelectedNodes | 0 | 0 | 0 | |
| selectNodes | 0 | 0 | 0 | |
| sendEdges | 0.004 | 0.000 | 0.000 | |
| sendNodes | 0 | 0 | 0 | |
| setCenter | 0.000 | 0.000 | 0.001 | |
| setDefaultBackgroundColor | 0.000 | 0.000 | 0.001 | |
| setDefaultEdgeColor | 0.000 | 0.000 | 0.001 | |
| setDefaultEdgeFontSize | 0.000 | 0.000 | 0.001 | |
| setDefaultEdgeLineWidth | 0 | 0 | 0 | |
| setDefaultEdgeReverseSelectionColor | 0 | 0 | 0 | |
| setDefaultEdgeSelectionColor | 0 | 0 | 0 | |
| setDefaultNodeBorderColor | 0 | 0 | 0 | |
| setDefaultNodeBorderWidth | 0 | 0 | 0 | |
| setDefaultNodeColor | 0 | 0 | 0 | |
| setDefaultNodeFontSize | 0.004 | 0.000 | 0.000 | |
| setDefaultNodeLabelColor | 0.000 | 0.000 | 0.001 | |
| setDefaultNodeReverseSelectionColor | 0.000 | 0.000 | 0.001 | |
| setDefaultNodeSelectionColor | 0.000 | 0.000 | 0.001 | |
| setDefaultNodeShape | 0.000 | 0.000 | 0.001 | |
| setDefaultNodeSize | 0 | 0 | 0 | |
| setEdgeAttributes | 0 | 0 | 0 | |
| setEdgeAttributesDirect | 0 | 0 | 0 | |
| setEdgeColorDirect | 0 | 0 | 0 | |
| setEdgeColorRule | 0 | 0 | 0 | |
| setEdgeFontSizeDirect | 0 | 0 | 0 | |
| setEdgeLabelColorDirect | 0.000 | 0.000 | 0.001 | |
| setEdgeLabelDirect | 0.000 | 0.000 | 0.001 | |
| setEdgeLabelOpacityDirect | 0.000 | 0.000 | 0.001 | |
| setEdgeLabelRule | 0.000 | 0.000 | 0.001 | |
| setEdgeLabelWidthDirect | 0 | 0 | 0 | |
| setEdgeLineStyleDirect | 0 | 0 | 0 | |
| setEdgeLineStyleRule | 0 | 0 | 0 | |
| setEdgeLineWidthDirect | 0 | 0 | 0 | |
| setEdgeLineWidthRule | 0 | 0 | 0 | |
| setEdgeOpacityDirect | 0 | 0 | 0 | |
| setEdgeOpacityRule | 0 | 0 | 0 | |
| setEdgeSourceArrowColorDirect | 0 | 0 | 0 | |
| setEdgeSourceArrowColorRule | 0 | 0 | 0 | |
| setEdgeSourceArrowOpacityDirect | 0.004 | 0.000 | 0.001 | |
| setEdgeSourceArrowRule | 0.000 | 0.000 | 0.001 | |
| setEdgeSourceArrowShapeDirect | 0.000 | 0.000 | 0.001 | |
| setEdgeTargetArrowColorDirect | 0.000 | 0.000 | 0.001 | |
| setEdgeTargetArrowColorRule | 0.000 | 0.000 | 0.001 | |
| setEdgeTargetArrowOpacityDirect | 0.000 | 0.000 | 0.001 | |
| setEdgeTargetArrowRule | 0 | 0 | 0 | |
| setEdgeTargetArrowShapeDirect | 0 | 0 | 0 | |
| setEdgeTooltipDirect | 0 | 0 | 0 | |
| setEdgeTooltipRule | 0 | 0 | 0 | |
| setGraph | 0 | 0 | 0 | |
| setLayoutProperties | 0 | 0 | 0 | |
| setNodeAttributes | 0.000 | 0.000 | 0.001 | |
| setNodeAttributesDirect | 0.000 | 0.000 | 0.001 | |
| setNodeBorderColorDirect | 0 | 0 | 0 | |
| setNodeBorderColorRule | 0 | 0 | 0 | |
| setNodeBorderOpacityDirect | 0.004 | 0.000 | 0.000 | |
| setNodeBorderWidthDirect | 0 | 0 | 0 | |
| setNodeBorderWidthRule | 0 | 0 | 0 | |
| setNodeColorDirect | 0 | 0 | 0 | |
| setNodeColorRule | 0.004 | 0.000 | 0.001 | |
| setNodeFillOpacityDirect | 0 | 0 | 0 | |
| setNodeFontSizeDirect | 0 | 0 | 0 | |
| setNodeHeightDirect | 0 | 0 | 0 | |
| setNodeImageDirect | 0.004 | 0.000 | 0.000 | |
| setNodeLabelColorDirect | 0 | 0 | 0 | |
| setNodeLabelDirect | 0 | 0 | 0 | |
| setNodeLabelOpacityDirect | 0 | 0 | 0 | |
| setNodeLabelRule | 0 | 0 | 0 | |
| setNodeOpacityDirect | 0 | 0 | 0 | |
| setNodeOpacityRule | 0 | 0 | 0 | |
| setNodePosition | 0.000 | 0.000 | 0.001 | |
| setNodeShapeDirect | 0.000 | 0.000 | 0.001 | |
| setNodeShapeRule | 0 | 0 | 0 | |
| setNodeSizeDirect | 0 | 0 | 0 | |
| setNodeSizeRule | 0 | 0 | 0 | |
| setNodeTooltipRule | 0 | 0 | 0 | |
| setNodeWidthDirect | 0 | 0 | 0 | |
| setTooltipDismissDelay | 0 | 0 | 0 | |
| setTooltipInitialDelay | 0 | 0 | 0 | |
| setVisualStyle | 0.004 | 0.000 | 0.000 | |
| setWindowSize | 0 | 0 | 0 | |
| setZoom | 0 | 0 | 0 | |
| showGraphicsDetails | 0 | 0 | 0 | |
| unhideAll | 0.004 | 0.000 | 0.001 | |