############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL RCy3 ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'RCy3' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'RCy3' finding HTML links ... done AddToGroup html RCy3 html RemoveFromGroup html UpdateAnnotationBoundedText html addAnnotationBoundedText html addAnnotationImage html addAnnotationShape html addAnnotationText html addCyEdges html addCyNodes html analyzeNetwork html applyFilter html bundleEdges html checkNotebookIsRunning html checkRunningRemote html clearEdgeBends html clearEdgePropertyBypass html clearNetworkCenterBypass html clearNetworkPropertyBypass html clearNetworkZoomBypass html clearNodeOpacityBypass html clearNodePropertyBypass html clearSelection html cloneNetwork html closeSession html collapseGroup html commandEcho html commandOpenDialog html commandPause html commandQuit html commandRunFile html commandSleep html commandsAPI html commandsGET html commandsHelp html commandsPOST html commandsRun html copyVisualStyle html createColumnFilter html createCompositeFilter html createDegreeFilter html createGraphFromNetwork html createGroup html createGroupByColumn html createIgraphFromNetwork html createNetworkFromDataFrames html createNetworkFromGraph html createNetworkFromIgraph html createSubnetwork html createVisualStyle html cybrowserClose html cybrowserDialog html cybrowserHide html cybrowserList html cybrowserSend html cybrowserShow html cybrowserVersion html cyrestAPI html cyrestDELETE html cyrestGET html cyrestPOST html cyrestPUT html cytoscapeApiVersions html cytoscapeFreeMemory html cytoscapeMemoryStatus html cytoscapeNumberOfCores html cytoscapePing html cytoscapeVersionInfo html deleteAllNetworks html deleteAnnotation html deleteDuplicateEdges html deleteGroup html deleteNetwork html deleteSelectedEdges html deleteSelectedNodes html deleteSelfLoops html deleteStyleMapping html deleteTableColumn html deleteVisualStyle html diffusionAdvanced html diffusionBasic html disableApp html doInitializeSandbox html doRequestRemote html doSetSandbox html dockPanel html dot-exportShowImage html dot-getDefaultSandbox html dot-getRequester html enableApp html expandGroup html exportFilters html exportImage html exportNetwork html exportNetworkToNDEx html exportVisualStyles html findRemoteCytoscape html fitContent html floatPanel html getAbsSandboxPath html getAllEdges html getAllNodes html getAllStyleMappings html getAnnotationList html getAppInformation html getAppStatus html getAppUpdates html getArrowShapes html getAvailableApps html getBackgroundColorDefault html getBrowserClientChannel html getBrowserClientJs html getCollectionList html getCollectionName html getCollectionNetworks html getCollectionSuid html getCurrentSandbox html getCurrentSandboxName html getCurrentSandboxPath html getCurrentStyle html getDefaultSandbox html getDefaultSandboxPath html getDisabledApps html getEdgeColor html getEdgeCount html getEdgeInfo html getEdgeLineStyle html getEdgeLineWidth html getEdgeProperty html getEdgeSelectionColorDefault html getEdgeTargetArrowShape html getFilterList html getFirstNeighbors html getGroupInfo html getInstalledApps html getJupyterBridgeURL html getLayoutNameMapping html getLayoutNames html getLayoutPropertyNames html getLayoutPropertyType html getLayoutPropertyValue html getLineStyles html getNetworkCenter html getNetworkCount html getNetworkList html getNetworkNDExId html getNetworkName html getNetworkProperty html getNetworkSuid html getNetworkViewSuid html getNetworkViews html getNetworkZoom html getNodeColor html getNodeCount html getNodeHeight html getNodePosition html getNodeProperty html getNodeSelectionColorDefault html getNodeShapes html getNodeSize html getNodeWidth html getNotebookIsRunning html getSandboxReinitialize html getSelectedEdgeCount html getSelectedEdges html getSelectedNodeCount html getSelectedNodes html getStyleDependencies html getStyleMapping html getTableColumnNames html getTableColumnTypes html getTableColumns html getTableValue html getUninstalledApps html getVisualPropertyDefault html getVisualPropertyNames html getVisualStyleNames html groupAnnotation html hideAllPanels html hideEdges html hideNodes html hidePanel html hideSelectedEdges html hideSelectedNodes html importFilters html importNetworkFromFile html importNetworkFromNDEx html importVisualStyles html installApp html invertEdgeSelection html invertNodeSelection html layoutCopycat html layoutNetwork html listGroups html loadTableData html lockNodeDimensions html makeSimpleGraph html makeSimpleIgraph html mapTableColumn html mapVisualProperty html matchArrowColorToEdge html mergeNetworks html notebookExportShowImage html notebookShowImage html openAppStore html openSession html paletteColorBrewerAccent html paletteColorBrewerBlues html paletteColorBrewerBrBG html paletteColorBrewerBuGn html paletteColorBrewerBuPu html paletteColorBrewerDark2 html paletteColorBrewerGnBu html paletteColorBrewerGreens html paletteColorBrewerGreys html paletteColorBrewerOrRd html paletteColorBrewerOranges html paletteColorBrewerPRGn html paletteColorBrewerPaired html paletteColorBrewerPastel1 html paletteColorBrewerPastel2 html paletteColorBrewerPiYG html paletteColorBrewerPuBu html paletteColorBrewerPuBuGn html paletteColorBrewerPuOr html paletteColorBrewerPuRd html paletteColorBrewerPurples html paletteColorBrewerRdBu html paletteColorBrewerRdPu html paletteColorBrewerRdYlBu html paletteColorBrewerReds html paletteColorBrewerSet1 html paletteColorBrewerSet2 html paletteColorBrewerSet3 html paletteColorBrewerYlGn html paletteColorBrewerYlGnBu html paletteColorBrewerYlOrBr html paletteColorBrewerYlOrRd html paletteColorRandom html removeNodeCustomGraphics html renameNetwork html renameTableColumn html resetDefaultSandbox html runningRemoteCheck html sandboxGetFileInfo html sandboxGetFrom html sandboxInitializer html sandboxRemove html sandboxRemoveFile html sandboxSendTo html sandboxSet html sandboxUrlTo html saveSession html selectAllEdges html selectAllNodes html selectEdges html selectEdgesAdjacentToSelectedNodes html selectEdgesConnectingSelectedNodes html selectFirstNeighbors html selectNodes html selectNodesConnectedBySelectedEdges html setBackgroundColorDefault html setCatchupFilterSecs html setCatchupNetworkSecs html setCurrentNetwork html setCurrentSandbox html setCurrentView html setDefaultSandbox html setDefaultSandboxPath html setEdgeColorBypass html setEdgeColorDefault html setEdgeColorMapping html setEdgeFontFaceBypass html setEdgeFontFaceDefault html setEdgeFontFaceMapping html setEdgeFontSizeBypass html setEdgeFontSizeDefault html setEdgeFontSizeMapping html setEdgeLabelBypass html setEdgeLabelColorBypass html setEdgeLabelColorDefault html setEdgeLabelColorMapping html setEdgeLabelDefault html setEdgeLabelMapping html setEdgeLabelOpacityBypass html setEdgeLabelOpacityDefault html setEdgeLabelOpacityMapping html setEdgeLineStyleBypass html setEdgeLineStyleDefault html setEdgeLineStyleMapping html setEdgeLineWidthBypass html setEdgeLineWidthDefault html setEdgeLineWidthMapping html setEdgeOpacityBypass html setEdgeOpacityDefault html setEdgeOpacityMapping html setEdgePropertyBypass html setEdgeSelectionColorDefault html setEdgeSourceArrowColorBypass html setEdgeSourceArrowColorDefault html setEdgeSourceArrowColorMapping html setEdgeSourceArrowMapping html setEdgeSourceArrowShapeBypass html setEdgeSourceArrowShapeDefault html setEdgeSourceArrowShapeMapping html setEdgeTargetArrowColorBypass html setEdgeTargetArrowColorDefault html setEdgeTargetArrowColorMapping html setEdgeTargetArrowMapping html setEdgeTargetArrowShapeBypass html setEdgeTargetArrowShapeDefault html setEdgeTargetArrowShapeMapping html setEdgeTooltipBypass html setEdgeTooltipDefault html setEdgeTooltipMapping html setLayoutProperties html setModelPropagationSecs html setNetworkCenterBypass html setNetworkPropertyBypass html setNetworkZoomBypass html setNodeBorderColorBypass html setNodeBorderColorDefault html setNodeBorderColorMapping html setNodeBorderOpacityBypass html setNodeBorderOpacityDefault html setNodeBorderOpacityMapping html setNodeBorderWidthBypass html setNodeBorderWidthDefault html setNodeBorderWidthMapping html setNodeColorBypass html setNodeColorDefault html setNodeColorMapping html setNodeComboOpacityMapping html setNodeCustomBarChart html setNodeCustomBoxChart html setNodeCustomHeatMapChart html setNodeCustomLineChart html setNodeCustomLinearGradient html setNodeCustomPieChart html setNodeCustomPosition html setNodeCustomRadialGradient html setNodeCustomRingChart html setNodeFillOpacityBypass html setNodeFillOpacityDefault html setNodeFillOpacityMapping html setNodeFontFaceBypass html setNodeFontFaceDefault html setNodeFontFaceMapping html setNodeFontSizeBypass html setNodeFontSizeDefault html setNodeFontSizeMapping html setNodeHeightBypass html setNodeHeightDefault html setNodeHeightMapping html setNodeLabelBypass html setNodeLabelColorBypass html setNodeLabelColorDefault html setNodeLabelColorMapping html setNodeLabelDefault html setNodeLabelMapping html setNodeLabelOpacityBypass html setNodeLabelOpacityDefault html setNodeLabelOpacityMapping html setNodeOpacityBypass html setNodePropertyBypass html setNodeSelectionColorDefault html setNodeShapeBypass html setNodeShapeDefault html setNodeShapeMapping html setNodeSizeBypass html setNodeSizeDefault html setNodeSizeMapping html setNodeTooltipBypass html setNodeTooltipDefault html setNodeTooltipMapping html setNodeWidthBypass html setNodeWidthDefault html setNodeWidthMapping html setNotebookIsRunning html setSandboxReinitialize html setStyleDependencies html setVisualPropertyDefault html setVisualStyle html spoofResponse-class html syncNodeCustomGraphicsSize html toggleGraphicsDetails html ungroupAnnotation html unhideAll html unhideEdges html unhideNodes html uninstallApp html updateAnnotationImage html updateAnnotationShape html updateAnnotationText html updateApp html updateGroupAnnotation html updateNetworkInNDEx html updateStyleDefaults html updateStyleMapping html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RCy3) Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'deltaGseg' is missing or broken done