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BioC 3.3: CHECK report for RCy3 on moscato2

This page was generated on 2016-01-05 11:26:02 -0800 (Tue, 05 Jan 2016).

Package 871/1123HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCy3 1.1.0
Paul Shannon , Tanja Muetze , Georgi Kolishovski
Snapshot Date: 2016-01-04 17:20:09 -0800 (Mon, 04 Jan 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCy3
Last Changed Rev: 109592 / Revision: 112163
Last Changed Date: 2015-10-13 12:59:53 -0700 (Tue, 13 Oct 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  ERROR 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ TIMEOUT ] OK 

Summary

Package: RCy3
Version: 1.1.0
Command: rm -rf RCy3.buildbin-libdir RCy3.Rcheck && mkdir RCy3.buildbin-libdir RCy3.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RCy3.buildbin-libdir RCy3_1.1.0.tar.gz >RCy3.Rcheck\00install.out 2>&1 && cp RCy3.Rcheck\00install.out RCy3-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=RCy3.buildbin-libdir --install="check:RCy3-install.out" --force-multiarch --no-vignettes --timings RCy3_1.1.0.tar.gz
StartedAt: 2016-01-05 05:52:51 -0800 (Tue, 05 Jan 2016)
EndedAt: 2016-01-05 06:32:52 -0800 (Tue, 05 Jan 2016)
EllapsedTime: 2400.2 seconds
RetCode: None
Status:  TIMEOUT  
CheckDir: RCy3.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RCy3.buildbin-libdir RCy3.Rcheck && mkdir RCy3.buildbin-libdir RCy3.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RCy3.buildbin-libdir RCy3_1.1.0.tar.gz >RCy3.Rcheck\00install.out 2>&1 && cp RCy3.Rcheck\00install.out RCy3-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=RCy3.buildbin-libdir --install="check:RCy3-install.out" --force-multiarch --no-vignettes --timings RCy3_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/RCy3.Rcheck'
* using R Under development (unstable) (2015-12-14 r69775)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RCy3/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RCy3' version '1.1.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'RCy3' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* loading checks for arch 'i386'
** 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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ...
** running examples for arch 'i386' ... [26m] OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
setNodeOpacityDirect            176.77  10.36  197.48
setNodeSizeDirect               114.89   5.42  127.87
setNodeLabelColorDirect         108.86   5.53  121.14
getNodeSize                     101.47   5.48  112.88
setNodeShapeDirect               64.09   3.34   70.77
setNodeLabelDirect               57.86   3.15   63.91
setNodeWidthDirect               56.52   3.24   63.92
setNodeImageDirect               55.69   3.83   62.66
setNodeLabelOpacityDirect        56.19   3.24   63.23
setNodeColorDirect               52.69   3.54   59.56
setNodeFontSizeDirect            50.65   3.18   57.27
setNodeHeightDirect              50.12   3.47   57.17
setNodeFillOpacityDirect         49.21   3.90   57.02
setNodeBorderColorDirect         50.38   2.69   56.05
setNodeBorderOpacityDirect       46.62   2.70   54.07
lockNodeDimensions               45.14   2.23   50.52
getGraphFromCyWindow              6.14   0.41    6.95
setEdgeOpacityDirect              4.87   0.23    5.56
setEdgeTargetArrowShapeDirect     3.08   0.12   12.80
setEdgeSourceArrowShapeDirect     2.92   0.20   12.63
setEdgeSourceArrowColorDirect     2.15   0.11    6.56
setEdgeTargetArrowColorDirect     2.12   0.11    6.58
setCenter                         2.06   0.09    8.22
setEdgeSourceArrowOpacityDirect   1.85   0.11    9.31
setWindowSize                     1.40   0.07    6.18
** running examples for arch 'x64' ...

RCy3.Rcheck/00install.out:


install for i386

* installing *source* package 'RCy3' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'RCy3' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RCy3' as RCy3_1.1.0.zip
* DONE (RCy3)

RCy3.Rcheck/examples_i386/RCy3-Ex.timings:

nameusersystemelapsed
CytoscapeConnection0.170.010.50
CytoscapeConnectionClass-class0.030.000.06
CytoscapeWindow0.150.000.39
CytoscapeWindowClass-class0.180.000.35
addCyEdge1.600.082.32
addCyNode1.180.081.57
addGraphToGraph1.690.062.17
clearSelection1.400.141.76
copyVisualStyle1.520.111.94
createWindowFromSelection1.230.032.06
cy2.edge.names0.050.000.09
cyPlot1.180.031.33
deleteAllWindows0.310.020.61
deleteEdgeAttribute1.450.111.87
deleteNodeAttribute1.440.061.79
deleteSelectedEdges1.360.131.76
deleteSelectedNodes1.430.011.69
deleteWindow1.310.111.86
demoSimpleGraph1.420.111.70
displayGraph1.140.161.51
dockPanel0.050.000.12
eda0.030.000.04
eda.names0.030.000.05
existing.CytoscapeWindow0.860.031.08
fitContent1.480.041.80
fitSelectedContent1.500.071.75
floatPanel0.110.000.26
getAdjacentEdgeNames0.070.000.08
getAllEdgeAttributes1.230.071.48
getAllEdges1.220.051.42
getAllNodeAttributes1.710.082.00
getAllNodes1.800.152.10
getArrowShapes0.060.000.13
getAttributeClassNames0.030.000.07
getCenter1.690.051.93
getDefaultBackgroundColor0.090.000.16
getDefaultEdgeReverseSelectionColor0.080.000.12
getDefaultEdgeSelectionColor0.090.000.13
getDefaultNodeReverseSelectionColor0.080.000.10
getDefaultNodeSelectionColor0.080.000.11
getDirectlyModifiableVisualProperties0.090.000.14
getEdgeAttribute1.470.061.74
getEdgeAttributeNames1.670.051.87
getEdgeCount1.930.082.14
getFirstNeighbors1.170.171.64
getGraph1.250.091.54
getGraphFromCyWindow6.140.416.95
getLayoutNameMapping0.040.000.09
getLayoutNames0.060.000.09
getLayoutPropertyNames0.090.000.13
getLayoutPropertyType0.300.030.37
getLayoutPropertyValue0.060.000.10
getLineStyles0.030.020.06
getNodeAttribute1.410.001.53
getNodeAttributeNames1.090.041.31
getNodeCount1.310.031.70
getNodePosition1.170.051.41
getNodeShapes0.010.010.09
getNodeSize101.47 5.48112.88
getSelectedEdgeCount1.820.062.05
getSelectedEdges1.620.081.82
getSelectedNodeCount1.500.091.73
getSelectedNodes1.620.101.89
getViewCoordinates1.140.061.39
getVisualStyleNames0.060.000.12
getWindowCount0.360.010.53
getWindowID1.170.031.45
getWindowList0.050.000.12
getZoom1.120.111.41
hideAllPanels0.160.020.31
hideNodes1.510.091.96
hidePanel0.120.000.17
hideSelectedEdges0.280.080.42
hideSelectedNodes0.410.020.52
initEdgeAttribute0.030.000.06
initNodeAttribute0.030.010.06
invertEdgeSelection0.190.000.28
invertNodeSelection0.530.030.67
layoutNetwork1.080.111.45
lockNodeDimensions45.14 2.2350.52
makeRandomGraph0.080.000.10
makeSimpleGraph0.080.000.09
noa0.060.000.08
noa.names0.050.000.06
ping0.060.020.09
pluginVersion0.050.000.10
predictTimeToDisplayGraph1.170.001.28
raiseWindow0.110.000.21
redraw0.170.000.27
restoreLayout1.640.122.17
saveImage1.200.051.39
saveLayout1.900.132.23
saveNetwork1.340.031.50
selectEdges1.520.071.84
selectFirstNeighborsOfSelectedNodes1.180.081.44
selectNodes0.420.030.56
sendEdges0.170.040.31
sendNodes0.210.000.31
setCenter2.060.098.22
setDefaultBackgroundColor0.100.000.14
setDefaultEdgeColor1.350.051.53
setDefaultEdgeFontSize1.640.091.92
setDefaultEdgeLineWidth1.400.171.78
setDefaultEdgeReverseSelectionColor1.360.061.57
setDefaultEdgeSelectionColor1.080.111.42
setDefaultEdgeSourceArrowColor1.420.061.69
setDefaultEdgeTargetArrowColor1.310.051.52
setDefaultNodeBorderColor1.480.081.92
setDefaultNodeBorderWidth1.360.091.88
setDefaultNodeColor1.200.021.68
setDefaultNodeFontSize1.530.081.75
setDefaultNodeLabelColor1.260.041.51
setDefaultNodeReverseSelectionColor1.190.071.47
setDefaultNodeSelectionColor1.310.041.56
setDefaultNodeShape1.460.081.74
setDefaultNodeSize1.410.061.63
setEdgeAttributes0.330.020.44
setEdgeAttributesDirect0.350.010.45
setEdgeColorDirect1.530.132.00
setEdgeColorRule1.500.061.72
setEdgeFontSizeDirect2.040.172.49
setEdgeLabelColorDirect1.330.071.64
setEdgeLabelDirect3.600.284.21
setEdgeLabelOpacityDirect3.260.203.76
setEdgeLabelRule1.360.081.78
setEdgeLineStyleDirect3.560.144.02
setEdgeLineStyleRule1.390.031.75
setEdgeLineWidthDirect1.920.062.23
setEdgeLineWidthRule1.370.051.53
setEdgeOpacityDirect4.870.235.56
setEdgeOpacityRule1.870.172.19
setEdgeSourceArrowColorDirect2.150.116.56
setEdgeSourceArrowColorRule0.270.000.36
setEdgeSourceArrowOpacityDirect1.850.119.31
setEdgeSourceArrowRule0.190.020.30
setEdgeSourceArrowShapeDirect 2.92 0.2012.63
setEdgeTargetArrowColorDirect2.120.116.58
setEdgeTargetArrowColorRule0.150.020.27
setEdgeTargetArrowOpacityDirect1.700.122.00
setEdgeTargetArrowRule0.290.020.43
setEdgeTargetArrowShapeDirect 3.08 0.1212.80
setEdgeTooltipDirect1.670.092.99
setEdgeTooltipRule1.270.081.56
setGraph0.110.020.20
setLayoutProperties0.060.000.11
setNodeAttributes0.390.040.50
setNodeAttributesDirect0.280.000.36
setNodeBorderColorDirect50.38 2.6956.05
setNodeBorderColorRule0.220.010.37
setNodeBorderOpacityDirect46.62 2.7054.07
setNodeBorderWidthDirect1.580.131.86
setNodeBorderWidthRule1.330.111.57
setNodeColorDirect52.69 3.5459.56
setNodeColorRule1.590.061.83
setNodeFillOpacityDirect49.21 3.9057.02
setNodeFontSizeDirect50.65 3.1857.27
setNodeHeightDirect50.12 3.4757.17
setNodeImageDirect55.69 3.8362.66
setNodeLabelColorDirect108.86 5.53121.14
setNodeLabelDirect57.86 3.1563.91
setNodeLabelOpacityDirect56.19 3.2463.23
setNodeLabelRule1.660.092.68
setNodeOpacityDirect176.77 10.36197.48
setNodeOpacityRule1.650.242.06
setNodePosition1.800.032.05
setNodeShapeDirect64.09 3.3470.77
setNodeShapeRule1.640.081.89
setNodeSizeDirect114.89 5.42127.87
setNodeSizeRule1.340.041.60
setNodeTooltipRule1.700.121.99
setNodeWidthDirect56.52 3.2463.92
setTooltipDismissDelay1.170.051.37
setTooltipInitialDelay1.160.051.54
setVisualStyle1.590.122.04
setWindowSize1.400.076.18
setZoom1.440.043.93
showGraphicsDetails0.050.000.09
unhideAll1.630.144.29

RCy3.Rcheck/examples_x64/RCy3-Ex.timings:

nameusersystemelapsed
CytoscapeConnection0.160.020.22
CytoscapeConnectionClass-class0.050.000.07
CytoscapeWindow0.120.000.22
CytoscapeWindowClass-class0.140.010.27
addCyEdge1.380.041.57
addCyNode1.570.032.06
addGraphToGraph1.530.071.89
clearSelection1.480.041.75
copyVisualStyle1.340.061.68
createWindowFromSelection1.410.082.40
cy2.edge.names0.060.000.14
cyPlot1.150.031.39
deleteAllWindows0.440.000.72
deleteEdgeAttribute1.090.061.37
deleteNodeAttribute1.170.091.41
deleteSelectedEdges1.140.071.53
deleteSelectedNodes1.230.091.53
deleteWindow1.450.111.95
demoSimpleGraph1.610.061.92
displayGraph1.250.091.54
dockPanel0.100.000.16
eda0.040.000.05
eda.names0.030.000.04
existing.CytoscapeWindow0.790.081.05
fitContent1.090.021.39
fitSelectedContent1.060.031.33
floatPanel0.090.000.22
getAdjacentEdgeNames0.030.000.05
getAllEdgeAttributes0.920.081.25
getAllEdges1.000.041.23
getAllNodeAttributes1.250.101.44
getAllNodes1.110.051.37
getArrowShapes0.060.000.13
getAttributeClassNames0.030.000.06
getCenter1.340.051.56
getDefaultBackgroundColor0.110.000.17
getDefaultEdgeReverseSelectionColor0.080.000.11
getDefaultEdgeSelectionColor0.060.000.10
getDefaultNodeReverseSelectionColor0.060.000.09
getDefaultNodeSelectionColor0.070.000.09
getDirectlyModifiableVisualProperties0.010.000.07
getEdgeAttribute1.110.081.40
getEdgeAttributeNames0.920.031.17
getEdgeCount1.080.041.31
getFirstNeighbors1.480.111.78
getGraph0.960.051.14
getGraphFromCyWindow4.280.364.94
getLayoutNameMapping0.010.000.08
getLayoutNames0.070.000.09
getLayoutPropertyNames0.060.010.13
getLayoutPropertyType0.370.000.44
getLayoutPropertyValue0.050.020.09
getLineStyles0.080.000.11
getNodeAttribute1.310.121.62
getNodeAttributeNames1.340.041.65
getNodeCount1.260.011.45
getNodePosition1.030.081.23
getNodeShapes0.040.000.09
getNodeSize 97.89 5.13110.78
getSelectedEdgeCount1.480.111.76
getSelectedEdges1.070.091.36
getSelectedNodeCount1.390.021.56
getSelectedNodes1.360.031.76
getViewCoordinates1.330.131.64
getVisualStyleNames0.060.000.13
getWindowCount0.370.030.56
getWindowID1.380.181.77
getWindowList0.080.000.16
getZoom1.180.071.40
hideAllPanels0.190.000.33
hideNodes1.640.071.87
hidePanel0.120.000.18
hideSelectedEdges0.410.000.52
hideSelectedNodes0.310.020.47
initEdgeAttribute0.050.000.08
initNodeAttribute0.010.000.03
invertEdgeSelection0.190.020.26
invertNodeSelection0.440.010.53
layoutNetwork1.140.061.39
lockNodeDimensions43.91 2.2749.34
makeRandomGraph0.060.000.10
makeSimpleGraph0.050.000.06
noa0.020.010.05
noa.names0.030.000.04
ping0.060.000.10
pluginVersion0.050.000.08
predictTimeToDisplayGraph1.180.061.41
raiseWindow0.140.020.25
redraw0.170.000.27
restoreLayout2.270.112.71
saveImage1.030.051.38
saveLayout1.630.061.88
saveNetwork1.460.091.67
selectEdges1.200.061.47
selectFirstNeighborsOfSelectedNodes1.280.031.48
selectNodes0.310.020.41
sendEdges0.180.020.31
sendNodes0.130.010.25
setCenter1.400.037.49
setDefaultBackgroundColor0.080.000.12
setDefaultEdgeColor1.300.171.58
setDefaultEdgeFontSize1.170.041.42
setDefaultEdgeLineWidth1.180.031.46
setDefaultEdgeReverseSelectionColor1.410.041.56
setDefaultEdgeSelectionColor0.950.051.16
setDefaultEdgeSourceArrowColor0.980.081.28
setDefaultEdgeTargetArrowColor0.970.111.26
setDefaultNodeBorderColor1.110.041.33
setDefaultNodeBorderWidth1.340.141.62
setDefaultNodeColor1.060.021.25
setDefaultNodeFontSize1.270.091.75
setDefaultNodeLabelColor1.370.051.56
setDefaultNodeReverseSelectionColor0.940.061.22
setDefaultNodeSelectionColor1.510.031.71
setDefaultNodeShape1.320.101.63
setDefaultNodeSize1.560.041.79
setEdgeAttributes0.320.020.42
setEdgeAttributesDirect0.390.000.47
setEdgeColorDirect1.340.091.59
setEdgeColorRule1.420.081.87
setEdgeFontSizeDirect1.500.081.82
setEdgeLabelColorDirect1.740.112.00
setEdgeLabelDirect3.690.174.50
setEdgeLabelOpacityDirect3.330.193.89
setEdgeLabelRule0.950.061.22
setEdgeLineStyleDirect3.660.164.11
setEdgeLineStyleRule1.360.091.80
setEdgeLineWidthDirect1.980.142.29
setEdgeLineWidthRule1.340.051.56
setEdgeOpacityDirect4.400.235.17
setEdgeOpacityRule1.610.051.80
setEdgeSourceArrowColorDirect1.610.116.09
setEdgeSourceArrowColorRule0.250.000.34
setEdgeSourceArrowOpacityDirect1.630.089.07
setEdgeSourceArrowRule0.300.000.38
setEdgeSourceArrowShapeDirect 3.27 0.1012.97
setEdgeTargetArrowColorDirect2.330.106.76
setEdgeTargetArrowColorRule0.210.010.33
setEdgeTargetArrowOpacityDirect1.920.132.24
setEdgeTargetArrowRule0.210.000.28
setEdgeTargetArrowShapeDirect 2.21 0.1111.91
setEdgeTooltipDirect1.390.112.72
setEdgeTooltipRule1.210.061.46
setGraph0.090.000.22
setLayoutProperties0.080.000.12
setNodeAttributes0.300.010.39
setNodeAttributesDirect0.250.020.34
setNodeBorderColorDirect48.91 2.6254.60
setNodeBorderColorRule0.430.050.56
setNodeBorderOpacityDirect53.26 2.9359.24
setNodeBorderWidthDirect1.060.061.32
setNodeBorderWidthRule1.330.171.67
setNodeColorDirect54.96 2.7561.37
setNodeColorRule1.170.081.52
setNodeFillOpacityDirect60.03 3.3566.57
setNodeFontSizeDirect53.93 2.6160.46