BioC 3.2: CHECK report for RCy3 on oaxaca

Package: RCy3

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RCy3_1.0.0.tar.gz

StartedAt: 2016-01-05 03:17:00 -0800 (Tue, 05 Jan 2016)

EndedAt: 2016-01-05 03:40:26 -0800 (Tue, 05 Jan 2016)

EllapsedTime: 1405.0 seconds

RetCode: 0

Status:  OK

CheckDir: RCy3.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RCy3_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/RCy3.Rcheck’
* using R version 3.2.3 (2015-12-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCy3/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCy3’ version ‘1.0.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘RCy3’ can be installed ... [7s/8s] 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [20m/22m] OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
setNodeOpacityDirect            151.008  3.158 164.488
setNodeSizeDirect               105.473  2.198 114.847
getNodeSize                      94.624  1.919 103.704
setNodeLabelColorDirect          90.244  1.847  98.798
setNodeWidthDirect               50.373  1.053  55.022
setNodeLabelOpacityDirect        49.683  1.013  54.067
setNodeShapeDirect               49.350  1.057  53.895
setNodeLabelDirect               48.686  1.021  53.016
setNodeFontSizeDirect            48.487  0.949  58.061
setNodeImageDirect               48.487  0.925  53.364
setNodeHeightDirect              48.074  0.954  54.459
setNodeFillOpacityDirect         47.135  0.914  51.470
setNodeColorDirect               46.150  0.970  50.253
setNodeBorderOpacityDirect       45.008  0.946  49.138
lockNodeDimensions               42.543  0.854  46.498
setNodeBorderColorDirect         40.771  0.906  44.707
getGraphFromCyWindow              4.645  0.117   5.223
setEdgeSourceArrowShapeDirect     2.590  0.063  11.977
setEdgeTargetArrowShapeDirect     2.524  0.062  11.876
setEdgeTargetArrowColorDirect     1.734  0.042   5.975
setEdgeSourceArrowColorDirect     1.707  0.042   5.970
setCenter                         1.601  0.052   6.852
setEdgeSourceArrowOpacityDirect   1.428  0.034   8.650
setWindowSize                     1.181  0.034   5.597
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [0s/0s]
 [1s/1s] 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: OK

* installing *source* package ‘RCy3’ ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
* DONE (RCy3)

name	user	system	elapsed
CytoscapeConnection	0.151	0.006	0.173
CytoscapeConnectionClass-class	0.037	0.002	0.070
CytoscapeWindow	0.131	0.004	0.199
CytoscapeWindowClass-class	0.155	0.004	0.257
addCyEdge	1.327	0.030	1.592
addCyNode	1.237	0.028	1.482
addGraphToGraph	1.459	0.034	1.741
clearSelection	1.382	0.034	1.797
copyVisualStyle	1.425	0.036	1.763
createWindowFromSelection	1.363	0.034	2.097
cy2.edge.names	0.037	0.002	0.151
cyPlot	0.824	0.020	0.974
deleteAllWindows	0.271	0.007	0.519
deleteEdgeAttribute	1.23	0.03	1.44
deleteNodeAttribute	1.170	0.026	1.394
deleteSelectedEdges	1.370	0.033	1.629
deleteSelectedNodes	1.401	0.034	1.697
deleteWindow	1.347	0.034	1.676
demoSimpleGraph	1.606	0.040	1.867
displayGraph	1.177	0.029	1.433
dockPanel	0.096	0.003	0.139
eda	0.037	0.001	0.040
eda.names	0.045	0.002	0.048
existing.CytoscapeWindow	1.092	0.027	1.289
fitContent	1.346	0.034	1.595
fitSelectedContent	1.366	0.033	1.610
floatPanel	0.095	0.003	0.199
getAdjacentEdgeNames	0.042	0.001	0.046
getAllEdgeAttributes	1.109	0.027	1.281
getAllEdges	1.116	0.029	1.319
getAllNodeAttributes	1.061	0.025	1.255
getAllNodes	1.072	0.025	1.272
getArrowShapes	0.060	0.003	0.098
getAttributeClassNames	0.036	0.001	0.041
getCenter	1.184	0.028	1.355
getDefaultBackgroundColor	0.061	0.003	0.103
getDefaultEdgeReverseSelectionColor	0.056	0.002	0.062
getDefaultEdgeSelectionColor	0.061	0.002	0.069
getDefaultNodeReverseSelectionColor	0.052	0.002	0.060
getDefaultNodeSelectionColor	0.063	0.002	0.071
getDirectlyModifiableVisualProperties	0.058	0.002	0.068
getEdgeAttribute	1.206	0.031	1.403
getEdgeAttributeNames	1.012	0.025	1.215
getEdgeCount	1.132	0.030	1.618
getFirstNeighbors	1.273	0.030	1.475
getGraph	1.012	0.026	1.213
getGraphFromCyWindow	4.645	0.117	5.223
getLayoutNameMapping	0.033	0.001	0.067
getLayoutNames	0.050	0.002	0.057
getLayoutPropertyNames	0.059	0.002	0.072
getLayoutPropertyType	0.293	0.015	0.350
getLayoutPropertyValue	0.067	0.002	0.076
getLineStyles	0.063	0.003	0.073
getNodeAttribute	1.155	0.029	1.319
getNodeAttributeNames	1.029	0.024	1.226
getNodeCount	1.071	0.026	1.255
getNodePosition	1.118	0.027	1.305
getNodeShapes	0.063	0.002	0.101
getNodeSize	94.624	1.919	103.704
getSelectedEdgeCount	1.179	0.027	1.363
getSelectedEdges	1.156	0.028	1.350
getSelectedNodeCount	1.220	0.029	1.414
getSelectedNodes	1.279	0.031	1.467
getViewCoordinates	1.083	0.026	1.262
getVisualStyleNames	0.063	0.003	0.099
getWindowCount	0.304	0.008	0.406
getWindowID	1.056	0.026	1.277
getWindowList	0.057	0.002	0.093
getZoom	1.135	0.026	1.277
hideAllPanels	0.154	0.004	0.256
hideNodes	1.315	0.030	1.478
hidePanel	0.099	0.003	0.151
hideSelectedEdges	0.327	0.008	0.387
hideSelectedNodes	0.385	0.009	0.473
initEdgeAttribute	0.030	0.001	0.055
initNodeAttribute	0.031	0.001	0.034
invertEdgeSelection	0.178	0.005	0.223
invertNodeSelection	0.404	0.010	0.492
layoutNetwork	1.141	0.026	1.310
lockNodeDimensions	42.543	0.854	46.498
makeRandomGraph	0.046	0.002	0.072
makeSimpleGraph	0.055	0.002	0.060
noa	0.039	0.001	0.043
noa.names	0.041	0.002	0.045
ping	0.053	0.002	0.061
pluginVersion	0.052	0.002	0.058
predictTimeToDisplayGraph	1.095	0.028	1.235
raiseWindow	0.122	0.004	0.184
redraw	0.140	0.004	0.204
restoreLayout	1.628	0.041	2.055
saveImage	1.158	0.028	1.323
saveLayout	1.775	0.045	2.001
saveNetwork	1.165	0.027	1.362
selectEdges	1.253	0.030	1.426
selectFirstNeighborsOfSelectedNodes	1.344	0.032	1.534
selectNodes	0.344	0.009	0.424
sendEdges	0.188	0.005	0.260
sendNodes	0.143	0.004	0.208
setCenter	1.601	0.052	6.852
setDefaultBackgroundColor	0.062	0.002	0.092
setDefaultEdgeColor	1.239	0.030	1.405
setDefaultEdgeFontSize	1.296	0.032	1.484
setDefaultEdgeLineWidth	1.224	0.030	1.467
setDefaultEdgeReverseSelectionColor	1.136	0.028	1.305
setDefaultEdgeSelectionColor	1.169	0.029	1.337
setDefaultEdgeSourceArrowColor	1.243	0.030	1.609
setDefaultEdgeTargetArrowColor	1.215	0.028	1.403
setDefaultNodeBorderColor	1.196	0.028	1.398
setDefaultNodeBorderWidth	1.209	0.027	1.393
setDefaultNodeColor	1.197	0.027	1.384
setDefaultNodeFontSize	1.214	0.027	1.390
setDefaultNodeLabelColor	1.168	0.028	1.347
setDefaultNodeReverseSelectionColor	1.129	0.028	1.307
setDefaultNodeSelectionColor	1.127	0.025	1.291
setDefaultNodeShape	1.297	0.032	1.477
setDefaultNodeSize	1.237	0.030	1.434
setEdgeAttributes	0.270	0.007	0.351
setEdgeAttributesDirect	0.275	0.008	0.354
setEdgeColorDirect	1.247	0.031	1.438
setEdgeColorRule	1.380	0.034	1.565
setEdgeFontSizeDirect	1.924	0.044	2.241
setEdgeLabelColorDirect	1.413	0.034	1.606
setEdgeLabelDirect	3.027	0.073	3.419
setEdgeLabelOpacityDirect	3.019	0.074	3.432
setEdgeLabelRule	1.210	0.029	1.379
setEdgeLineStyleDirect	3.332	0.082	3.776
setEdgeLineStyleRule	1.249	0.030	1.421
setEdgeLineWidthDirect	1.379	0.034	1.599
setEdgeLineWidthRule	1.261	0.029	1.435
setEdgeOpacityDirect	4.222	0.098	4.767
setEdgeOpacityRule	1.477	0.035	1.699
setEdgeSourceArrowColorDirect	1.707	0.042	5.970
setEdgeSourceArrowColorRule	0.193	0.005	0.280
setEdgeSourceArrowOpacityDirect	1.428	0.034	8.650
setEdgeSourceArrowRule	0.234	0.006	0.300
setEdgeSourceArrowShapeDirect	2.590	0.063	11.977
setEdgeTargetArrowColorDirect	1.734	0.042	5.975
setEdgeTargetArrowColorRule	0.210	0.006	0.281
setEdgeTargetArrowOpacityDirect	1.490	0.035	1.963
setEdgeTargetArrowRule	0.232	0.006	0.306
setEdgeTargetArrowShapeDirect	2.524	0.062	11.876
setEdgeTooltipDirect	1.298	0.031	2.481
setEdgeTooltipRule	1.236	0.029	1.419
setGraph	0.128	0.004	0.198
setLayoutProperties	0.065	0.002	0.095
setNodeAttributes	0.293	0.008	0.347
setNodeAttributesDirect	0.222	0.006	0.296
setNodeBorderColorDirect	40.771	0.906	44.707
setNodeBorderColorRule	0.281	0.008	0.377
setNodeBorderOpacityDirect	45.008	0.946	49.138
setNodeBorderWidthDirect	1.141	0.026	1.308
setNodeBorderWidthRule	1.235	0.030	1.408
setNodeColorDirect	46.150	0.970	50.253
setNodeColorRule	1.212	0.026	1.403
setNodeFillOpacityDirect	47.135	0.914	51.470
setNodeFontSizeDirect	48.487	0.949	58.061
setNodeHeightDirect	48.074	0.954	54.459
setNodeImageDirect	48.487	0.925	53.364
setNodeLabelColorDirect	90.244	1.847	98.798
setNodeLabelDirect	48.686	1.021	53.016
setNodeLabelOpacityDirect	49.683	1.013	54.067
setNodeLabelRule	1.674	0.036	1.913
setNodeOpacityDirect	151.008	3.158	164.488
setNodeOpacityRule	0.984	0.029	1.162
setNodePosition	0.885	0.026	1.085
setNodeShapeDirect	49.350	1.057	53.895
setNodeShapeRule	1.266	0.029	1.444
setNodeSizeDirect	105.473	2.198	114.847
setNodeSizeRule	1.306	0.030	1.503
setNodeTooltipRule	1.328	0.030	1.587
setNodeWidthDirect	50.373	1.053	55.022
setTooltipDismissDelay	1.293	0.032	1.479
setTooltipInitialDelay	1.276	0.031	1.452
setVisualStyle	1.698	0.043	1.960
setWindowSize	1.181	0.034	5.597
setZoom	1.251	0.037	3.439
showGraphicsDetails	0.035	0.002	0.060
unhideAll	1.398	0.039	3.597