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BioC 3.4: CHECK report for RCyjs on zin1

This page was generated on 2016-09-21 03:39:50 -0700 (Wed, 21 Sep 2016).

Package 989/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCyjs 1.5.7
Paul Shannon
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCyjs
Last Changed Rev: 119087 / Revision: 121152
Last Changed Date: 2016-07-01 17:33:06 -0700 (Fri, 01 Jul 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ ERROR ]
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
morelia Mac OS X Mavericks (10.9.5) / x86_64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...

Summary

Package: RCyjs
Version: 1.5.7
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RCyjs_1.5.7.tar.gz
StartedAt: 2016-09-20 11:21:21 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 11:55:15 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 2033.5 seconds
RetCode: 1
Status:  ERROR 
CheckDir: RCyjs.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RCyjs_1.5.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/RCyjs.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 ‘RCyjs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCyjs’ version ‘1.5.7’
* 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 ‘RCyjs’ 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
* 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 ... NOTE
createTestGraph: no visible global function definition for ‘as’
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
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 ... WARNING
Undocumented code objects:
  ‘getNodeSize’
Undocumented S4 methods:
  generic 'getNodeSize' and siglist 'RCyjsClass'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... ERROR
Running examples in ‘RCyjs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RCyjsClass
> ### Title: RCyjs: Interactive R/browser network visualization, using
> ###   cytoscape.js
> ### Aliases: RCyjs class:RCyjsClass RCyjsClass-class show,RCyjsClass-method
> ###   setGraph setGraph,RCyjsClass-method \S4method{setGraph}{RCyjsClass}
> ###   addGraph addGraph,RCyjsClass-method \S4method{addGraph}{RCyjsClass}
> ###   httpAddGraph httpAddGraph,RCyjsClass-method
> ###   \S4method{httpAddGraph}{RCyjsClass} httpSetStyle
> ###   httpSetStyle,RCyjsClass-method \S4method{httpSetStyle}{RCyjsClass}
> ###   setNodeAttributes setNodeAttributes,RCyjsClass-method
> ###   \S4method{setNodeAttributes}{RCyjsClass} getNodeCount
> ###   getNodeCount,RCyjsClass-method \S4method{getNodeCount}{RCyjsClass}
> ###   getEdgeCount getEdgeCount,RCyjsClass-method
> ###   \S4method{getEdgeCount}{RCyjsClass} getNodes
> ###   getNodes,RCyjsClass-method \S4method{getNodes}{RCyjsClass}
> ###   setDefaultNodeSize setDefaultNodeSize,RCyjsClass-method
> ###   \S4method{setDefaultNodeSize}{RCyjsClass} setDefaultNodeWidth
> ###   setDefaultNodeWidth,RCyjsClass-method
> ###   \S4method{setDefaultNodeWidth}{RCyjsClass} setDefaultNodeHeight
> ###   setDefaultNodeHeight,RCyjsClass-method
> ###   \S4method{setDefaultNodeHeight}{RCyjsClass} setDefaultNodeColor
> ###   setDefaultNodeColor,RCyjsClass-method
> ###   \S4method{setDefaultNodeColor}{RCyjsClass} setDefaultNodeShape
> ###   setDefaultNodeShape,RCyjsClass-method
> ###   \S4method{setDefaultNodeShape}{RCyjsClass} setDefaultNodeFontColor
> ###   setDefaultNodeFontColor,RCyjsClass-method
> ###   \S4method{setDefaultNodeFontColor}{RCyjsClass} setDefaultNodeFontSize
> ###   setDefaultNodeFontSize,RCyjsClass-method
> ###   \S4method{setDefaultNodeFontSize}{RCyjsClass}
> ###   setDefaultNodeBorderWidth setDefaultNodeBorderWidth,RCyjsClass-method
> ###   \S4method{setDefaultNodeBorderWidth}{RCyjsClass}
> ###   setDefaultNodeBorderColor setDefaultNodeBorderColor,RCyjsClass-method
> ###   \S4method{setDefaultNodeBorderColor}{RCyjsClass}
> ###   setDefaultEdgeFontSize setDefaultEdgeFontSize,RCyjsClass-method
> ###   \S4method{setDefaultEdgeFontSize}{RCyjsClass}
> ###   setDefaultEdgeTargetArrowShape
> ###   setDefaultEdgeTargetArrowShape,RCyjsClass-method
> ###   \S4method{setDefaultEdgeTargetArrowShape}{RCyjsClass}
> ###   setDefaultEdgeColor setDefaultEdgeColor,RCyjsClass-method
> ###   \S4method{setDefaultEdgeColor}{RCyjsClass}
> ###   setDefaultEdgeTargetArrowColor
> ###   setDefaultEdgeTargetArrowColor,RCyjsClass-method
> ###   \S4method{setDefaultEdgeTargetArrowColor}{RCyjsClass}
> ###   setDefaultEdgeFontSize setDefaultEdgeFontSize,RCyjsClass-method
> ###   \S4method{setDefaultEdgeFontSize}{RCyjsClass} setDefaultEdgeWidth
> ###   setDefaultEdgeWidth,RCyjsClass-method
> ###   \S4method{setDefaultEdgeWidth}{RCyjsClass} setDefaultEdgeLineColor
> ###   setDefaultEdgeLineColor,RCyjsClass-method
> ###   \S4method{setDefaultEdgeLineColor}{RCyjsClass} setDefaultEdgeFont
> ###   setDefaultEdgeFont,RCyjsClass-method
> ###   \S4method{setDefaultEdgeFont}{RCyjsClass} setDefaultEdgeFontWeight
> ###   setDefaultEdgeFontWeight,RCyjsClass-method
> ###   \S4method{setDefaultEdgeFontWeight}{RCyjsClass}
> ###   setDefaultEdgeTextOpacity setDefaultEdgeTextOpacity,RCyjsClass-method
> ###   \S4method{setDefaultEdgeTextOpacity}{RCyjsClass}
> ###   setDefaultEdgeLineStyle setDefaultEdgeLineStyle,RCyjsClass-method
> ###   \S4method{setDefaultEdgeLineStyle}{RCyjsClass} setDefaultEdgeOpacity
> ###   setDefaultEdgeOpacity,RCyjsClass-method
> ###   \S4method{setDefaultEdgeOpacity}{RCyjsClass}
> ###   setDefaultEdgeSourceArrowColor
> ###   setDefaultEdgeSourceArrowColor,RCyjsClass-method
> ###   \S4method{setDefaultEdgeSourceArrowColor}{RCyjsClass}
> ###   setDefaultEdgeSourceArrowShape
> ###   setDefaultEdgeSourceArrowShape,RCyjsClass-method
> ###   \S4method{setDefaultEdgeSourceArrowShape}{RCyjsClass}
> ###   getSelectedNodes getSelectedNodes,RCyjsClass-method
> ###   \S4method{getSelectedNodes}{RCyjsClass} invertNodeSelection
> ###   invertNodeSelection,RCyjsClass-method
> ###   \S4method{invertNodeSelection}{RCyjsClass} hideSelectedNodes
> ###   hideSelectedNodes,RCyjsClass-method
> ###   \S4method{hideSelectedNodes}{RCyjsClass} deleteSelectedNodes
> ###   deleteSelectedNodes,RCyjsClass-method
> ###   \S4method{deleteSelectedNodes}{RCyjsClass} setNodeLabelRule
> ###   setNodeLabelRule,RCyjsClass-method
> ###   \S4method{setNodeLabelRule}{RCyjsClass} setNodeLabelAlignment
> ###   setNodeLabelAlignment,RCyjsClass-method
> ###   \S4method{setNodeLabelAlignment}{RCyjsClass} setNodeSizeRule
> ###   setNodeSizeRule,RCyjsClass-method
> ###   \S4method{setNodeSizeRule}{RCyjsClass} setNodeColorRule
> ###   setNodeColorRule,RCyjsClass-method
> ###   \S4method{setNodeColorRule}{RCyjsClass} setNodeShapeRule
> ###   setNodeShapeRule,RCyjsClass-method
> ###   \S4method{setNodeShapeRule}{RCyjsClass} setEdgeStyle
> ###   setEdgeStyle,RCyjsClass-method \S4method{setEdgeStyle}{RCyjsClass}
> ###   setEdgeColorRule setEdgeColorRule,RCyjsClass-method
> ###   \S4method{setEdgeColorRule}{RCyjsClass} setEdgeWidthRule
> ###   setEdgeWidthRule,RCyjsClass-method
> ###   \S4method{setEdgeWidthRule}{RCyjsClass} setEdgeTargetArrowShapeRule
> ###   setEdgeTargetArrowShapeRule,RCyjsClass-method
> ###   \S4method{setEdgeTargetArrowShapeRule}{RCyjsClass}
> ###   setEdgeTargetArrowColorRule
> ###   setEdgeTargetArrowColorRule,RCyjsClass-method
> ###   \S4method{setEdgeTargetArrowColorRule}{RCyjsClass}
> ###   setEdgeSourceArrowShapeRule
> ###   setEdgeSourceArrowShapeRule,RCyjsClass-method
> ###   \S4method{setEdgeSourceArrowShapeRule}{RCyjsClass}
> ###   setEdgeSourceArrowColorRule
> ###   setEdgeSourceArrowColorRule,RCyjsClass-method
> ###   \S4method{setEdgeSourceArrowColorRule}{RCyjsClass} redraw
> ###   redraw,RCyjsClass-method \S4method{redraw}{RCyjsClass} hideAllEdges
> ###   hideAllEdges,RCyjsClass-method \S4method{hideAllEdges}{RCyjsClass}
> ###   hideEdges hideEdges,RCyjsClass-method
> ###   \S4method{hideEdges}{RCyjsClass} showAllEdges
> ###   showAllEdges,RCyjsClass-method \S4method{showAllEdges}{RCyjsClass}
> ###   showAll showAll,RCyjsClass-method \S4method{showAll}{RCyjsClass}
> ###   showEdges showEdges,RCyjsClass-method
> ###   \S4method{showEdges}{RCyjsClass} layoutStrategies
> ###   layoutStrategies,RCyjsClass-method
> ###   \S4method{layoutStrategies}{RCyjsClass} layout
> ###   layout,RCyjsClass-method \S4method{layout}{RCyjsClass} hAlign
> ###   hAlign,RCyjsClass-method \S4method{hAlign}{RCyjsClass} vAlign
> ###   vAlign,RCyjsClass-method \S4method{vAlign}{RCyjsClass}
> ###   layoutSelectionInGrid layoutSelectionInGrid,RCyjsClass-method
> ###   \S4method{layoutSelectionInGrid}{RCyjsClass}
> ###   layoutSelectionInGridInferAnchor
> ###   layoutSelectionInGridInferAnchor,RCyjsClass-method
> ###   \S4method{layoutSelectionInGridInferAnchor}{RCyjsClass} getPosition
> ###   getPosition,RCyjsClass-method \S4method{getPosition}{RCyjsClass}
> ###   setPosition setPosition,RCyjsClass-method
> ###   \S4method{setPosition}{RCyjsClass} getSize getSize,RCyjsClass-method
> ###   \S4method{getSize}{RCyjsClass} getLayout getLayout,RCyjsClass-method
> ###   \S4method{getLayout}{RCyjsClass} saveLayout
> ###   saveLayout,RCyjsClass-method \S4method{saveLayout}{RCyjsClass}
> ###   restoreLayout restoreLayout,RCyjsClass-method
> ###   \S4method{restoreLayout}{RCyjsClass} getJSON
> ###   getJSON,RCyjsClass-method \S4method{getJSON}{RCyjsClass} fit
> ###   fit,RCyjsClass-method \S4method{fit}{RCyjsClass} fitContent
> ###   fitContent,RCyjsClass-method \S4method{fitContent}{RCyjsClass}
> ###   fitSelectedContent fitSelectedContent,RCyjsClass-method
> ###   \S4method{fitSelectedContent}{RCyjsClass} selectNodes
> ###   selectNodes,RCyjsClass-method \S4method{selectNodes}{RCyjsClass} sfn
> ###   sfn,RCyjsClass-method \S4method{sfn}{RCyjsClass} clearSelection
> ###   clearSelection,RCyjsClass-method
> ###   \S4method{clearSelection}{RCyjsClass} getZoom
> ###   getZoom,RCyjsClass-method \S4method{getZoom}{RCyjsClass} setZoom
> ###   setZoom,RCyjsClass-method \S4method{setZoom}{RCyjsClass}
> ###   setBackgroundColor setBackgroundColor,RCyjsClass-method
> ###   \S4method{setBackgroundColor}{RCyjsClass} biocGraphToCytoscapeJSON
> ###   createTestGraph eda edaNames noa noaNames simpleDemoGraph
> ### Keywords: classes methods
> 
> ### ** Examples
> 
>    library(RCyjs)
> 
>    g <- simpleDemoGraph()  # a 3-node, 3-edge graph with some node and edge attributes
>    noaNames(g)
[1] "type"  "lfc"   "label" "count"
>    edaNames(g)
[1] "edgeType" "score"    "misc"    
> 
>    rcy <- RCyjs(portRange=9047:9057, quiet=TRUE, graph=g);
Failed to connect to Mir: Failed to connect to server socket: No such file or directory
Unable to init server: Could not connect: Connection refused
Error: cannot open display: :1.0
Error: totalWait < maxWaitPermitted is not TRUE
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  1 Test Suite : 
  RCyjs RUnit Tests - 1 test function, 1 error, 0 failures
  ERROR in /home/biocbuild/bbs-3.4-bioc/meat/RCyjs.Rcheck/RCyjs/unitTests/test_RCyjs.R: Error while sourcing  /home/biocbuild/bbs-3.4-bioc/meat/RCyjs.Rcheck/RCyjs/unitTests/test_RCyjs.R : Error : totalWait < maxWaitPermitted is not TRUE
  
  Test files with failing tests
  
     test_RCyjs.R 
       /home/biocbuild/bbs-3.4-bioc/meat/RCyjs.Rcheck/RCyjs/unitTests/test_RCyjs.R 
  
  
  Error in BiocGenerics:::testPackage("RCyjs") : 
    unit tests failed for package RCyjs
  Execution halted
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘org.Hs.eg.db’
* 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: 2 ERRORs, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/RCyjs.Rcheck/00check.log’
for details.

runTests.Rout.fail:


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("RCyjs")

Attaching package: 'BrowserViz'

The following object is masked from 'package:jsonlite':

    toJSON


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min


Attaching package: 'RCyjs'

The following object is masked from 'package:graphics':

    layout

[1] "--- test.constructor"
Failed to connect to Mir: Failed to connect to server socket: No such file or directory
Unable to init server: Could not connect: Connection refused
Error: cannot open display: :1.0
Error : totalWait < maxWaitPermitted is not TRUE


RUNIT TEST PROTOCOL -- Tue Sep 20 11:55:11 2016 
*********************************************** 
Number of test functions: 1 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
RCyjs RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in /home/biocbuild/bbs-3.4-bioc/meat/RCyjs.Rcheck/RCyjs/unitTests/test_RCyjs.R: Error while sourcing  /home/biocbuild/bbs-3.4-bioc/meat/RCyjs.Rcheck/RCyjs/unitTests/test_RCyjs.R : Error : totalWait < maxWaitPermitted is not TRUE

Test files with failing tests

   test_RCyjs.R 
     /home/biocbuild/bbs-3.4-bioc/meat/RCyjs.Rcheck/RCyjs/unitTests/test_RCyjs.R 


Error in BiocGenerics:::testPackage("RCyjs") : 
  unit tests failed for package RCyjs
Execution halted

RCyjs.Rcheck/00install.out:

* installing *source* package ‘RCyjs’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘layout’ in package ‘RCyjs’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RCyjs)

RCyjs.Rcheck/RCyjs-Ex.timings:

nameusersystemelapsed