RCy 1.7.11 edgeAttributes bug - RCytoscape

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RCy 1.7.11 edgeAttributes bug

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Robert M. Flight

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More options Jul 23 2012, 10:40 am

From: "Robert M. Flight" <rfligh...@gmail.com>

Date: Mon, 23 Jul 2012 10:40:31 -0400

Local: Mon, Jul 23 2012 10:40 am

Subject: RCy 1.7.11 edgeAttributes bug

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In RCy 1.7.11, adding edge attributes causes a failure, in that the
attributes cannot be sent to the Cytoscape connection.

Examples below.

-Robert

Robert M. Flight, Ph.D.
robertmflight.blogspot.com
bioinformatics.louisville.edu/lab
github.com/rmflight/general/wiki

The most exciting phrase to hear in science, the one that heralds new
discoveries, is not "Eureka!" (I found it!) but "That's funny ..." -
Isaac Asimov

> options(save.defaults=list(compress="xz"), stringsAsFactors=FALSE)
> require(RCytoscape)

Loading required package: RCytoscape
Loading required package: graph
Loading required package: XMLRPC
Warning message:
package ‘RCytoscape’ was built under R version 2.15.1

- Show quoted text -

entering RCytoscape::displayGraph
estimated displayGraph time: 15.1 seconds
adding 3 nodes...
sending 3 nodes
ending sendNodes
adding 3 edges...
transforming (3) graph edges to nodePairTable
sending 3 edges
adding node attributes...
[1] "type"
[1] "lfc"
[1] "label"
[1] "count"
adding edge attributes...
[1] "edgeType"
entering setEdgeAttributesDirect, edgeType, with 3 names and 3 values
Error in file(file, ifelse(append, "a", "w")) :
cannot open the connection
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
cannot open file 'data': Permission denied

- Show quoted text -

> sessionInfo()

R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] RCytoscape_1.7.11 XMLRPC_0.2-4 graph_1.35.1

loaded via a namespace (and not attached):
[1] BiocGenerics_0.3.0 RCurl_1.91-1.1 tools_2.15.0 XML_3.9-4.1

> Sys.time()

[1] "2012-07-23 10:38:05 EDT"

Paul Shannon

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More options Jul 23 2012, 11:25 am

From: Paul Shannon <paul.thurmond.shan...@gmail.com>

Date: Mon, 23 Jul 2012 08:25:55 -0700

Local: Mon, Jul 23 2012 11:25 am

Subject: Re: RCy 1.7.11 edgeAttributes bug

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Hi Robert,

This is a mystery. I know of no call to append in RCytoscape. Could you call 'traceback ()' when the error occurs? That should reveal where the failed call is coming from.

I checked in your improvements to "remove.redundancies.in.undirected.graph" on Saturday. They should show up as 1.17.12 by tomorrow morning.

Looking forward to seeing what traceback () says --

- Paul

On Jul 23, 2012, at 7:40 AM, Robert M. Flight wrote:

- Show quoted text -

> In RCy 1.7.11, adding edge attributes causes a failure, in that the
> attributes cannot be sent to the Cytoscape connection.

> Examples below.

> -Robert

> Robert M. Flight, Ph.D.
> robertmflight.blogspot.com
> bioinformatics.louisville.edu/lab
> github.com/rmflight/general/wiki

> The most exciting phrase to hear in science, the one that heralds new
> discoveries, is not "Eureka!" (I found it!) but "That's funny ..." -
> Isaac Asimov

>> options(save.defaults=list(compress="xz"), stringsAsFactors=FALSE)
>> require(RCytoscape)
> Loading required package: RCytoscape
> Loading required package: graph
> Loading required package: XMLRPC
> Warning message:
> package ‘RCytoscape’ was built under R version 2.15.1
>> # note that is directly from Pauls 'makeSimpleGraph' function
>> g = new("graphNEL", edgemode = "directed")
>> nodeDataDefaults(g, attr = "type") = "undefined"
>> attr(nodeDataDefaults(g, attr = "type"), "class") = "STRING"
>> nodeDataDefaults(g, attr = "lfc") = 1
>> attr(nodeDataDefaults(g, attr = "lfc"), "class") = "DOUBLE"
>> nodeDataDefaults(g, attr = "label") = "default node label"
>> attr(nodeDataDefaults(g, attr = "label"), "class") = "STRING"
>> nodeDataDefaults(g, attr = "count") = "0"
>> attr(nodeDataDefaults(g, attr = "count"), "class") = "INTEGER"
>> edgeDataDefaults(g, attr = "edgeType") = "undefined"
>> attr(edgeDataDefaults(g, attr = "edgeType"), "class") = "STRING"
>> edgeDataDefaults(g, attr = "score") = 0
>> attr(edgeDataDefaults(g, attr = "score"), "class") = "DOUBLE"
>> edgeDataDefaults(g, attr = "misc") = ""
>> attr(edgeDataDefaults(g, attr = "misc"), "class") = "STRING"
>> g = graph::addNode("A", g)
>> g = graph::addNode("B", g)
>> g = graph::addNode("C", g)
>> nodeData(g, "A", "type") = "kinase"
>> nodeData(g, "B", "type") = "transcription factor"
>> nodeData(g, "C", "type") = "glycoprotein"
>> nodeData(g, "A", "lfc") = "-3.0"
>> nodeData(g, "B", "lfc") = "0.0"
>> nodeData(g, "C", "lfc") = "3.0"
>> nodeData(g, "A", "count") = "2"
>> nodeData(g, "B", "count") = "30"
>> nodeData(g, "C", "count") = "100"
>> nodeData(g, "A", "label") = "Gene A"
>> nodeData(g, "B", "label") = "Gene B"
>> nodeData(g, "C", "label") = "Gene C"
>> g = graph::addEdge("A", "B", g)
>> g = graph::addEdge("B", "C", g)
>> g = graph::addEdge("C", "A", g)
>> edgeData(g, "A", "B", "edgeType") = "phosphorylates"
>> edgeData(g, "B", "C", "edgeType") = "synthetic lethal"
>> edgeData(g, "A", "B", "score") = 35
>> edgeData(g, "B", "C", "score") = -12
>> cw1 <- CytoscapeWindow("test1", graph=g, rpcPort=9000)
>> displayGraph(cw1)
> entering RCytoscape::displayGraph
> estimated displayGraph time: 15.1 seconds
> adding 3 nodes...
> sending 3 nodes
> ending sendNodes
> adding 3 edges...
> transforming (3) graph edges to nodePairTable
> sending 3 edges
> adding node attributes...
> [1] "type"
> [1] "lfc"
> [1] "label"
> [1] "count"
> adding edge attributes...
> [1] "edgeType"
> entering setEdgeAttributesDirect, edgeType, with 3 names and 3 values
> Error in file(file, ifelse(append, "a", "w")) :
> cannot open the connection
> In addition: Warning message:
> In file(file, ifelse(append, "a", "w")) :
> cannot open file 'data': Permission denied
>> g = new("graphNEL", edgemode = "directed")
>> nodeDataDefaults(g, attr = "type") = "undefined"
>> attr(nodeDataDefaults(g, attr = "type"), "class") = "STRING"
>> nodeDataDefaults(g, attr = "lfc") = 1
>> attr(nodeDataDefaults(g, attr = "lfc"), "class") = "DOUBLE"
>> nodeDataDefaults(g, attr = "label") = "default node label"
>> attr(nodeDataDefaults(g, attr = "label"), "class") = "STRING"
>> nodeDataDefaults(g, attr = "count") = "0"
>> attr(nodeDataDefaults(g, attr = "count"), "class") = "INTEGER"
>> # edgeDataDefaults(g, attr = "edgeType") = "undefined"
>> # attr(edgeDataDefaults(g, attr = "edgeType"), "class") = "STRING"
>> # edgeDataDefaults(g, attr = "score") = 0
>> # attr(edgeDataDefaults(g, attr = "score"), "class") = "DOUBLE"
>> # edgeDataDefaults(g, attr = "misc") = ""
>> # attr(edgeDataDefaults(g, attr = "misc"), "class") = "STRING"
>> g = graph::addNode("A", g)
>> g = graph::addNode("B", g)
>> g = graph::addNode("C", g)
>> nodeData(g, "A", "type") = "kinase"
>> nodeData(g, "B", "type") = "transcription factor"
>> nodeData(g, "C", "type") = "glycoprotein"
>> nodeData(g, "A", "lfc") = "-3.0"
>> nodeData(g, "B", "lfc") = "0.0"
>> nodeData(g, "C", "lfc") = "3.0"
>> nodeData(g, "A", "count") = "2"
>> nodeData(g, "B", "count") = "30"
>> nodeData(g, "C", "count") = "100"
>> nodeData(g, "A", "label") = "Gene A"
>> nodeData(g, "B", "label") = "Gene B"
>> nodeData(g, "C", "label") = "Gene C"
>> g = graph::addEdge("A", "B", g)
>> g = graph::addEdge("B", "C", g)
>> g = graph::addEdge("C", "A", g)
>> # edgeData(g, "A", "B", "edgeType") = "phosphorylates"
>> # edgeData(g, "B", "C", "edgeType") = "synthetic lethal"
>> cw2 <- CytoscapeWindow("test2", graph=g, rpcPort=9000)
>> displayGraph(cw2)
> entering RCytoscape::displayGraph
> estimated displayGraph time: 15.1 seconds
> adding 3 nodes...
> sending 3 nodes
> ending sendNodes
> adding 3 edges...
> transforming (3) graph edges to nodePairTable
> sending 3 edges
> adding node attributes...
> [1] "type"
> [1] "lfc"
> [1] "label"
> [1] "count"
> adding edge attributes...
>> g = new("graphNEL", edgemode = "directed")
>> nodeDataDefaults(g, attr = "type") = "undefined"
>> attr(nodeDataDefaults(g, attr = "type"), "class") = "STRING"
>> nodeDataDefaults(g, attr = "lfc") = 1
>> attr(nodeDataDefaults(g, attr = "lfc"), "class") = "DOUBLE"
>> nodeDataDefaults(g, attr = "label") = "default node label"
>> attr(nodeDataDefaults(g, attr = "label"), "class") = "STRING"
>> nodeDataDefaults(g, attr = "count") = "0"
>> attr(nodeDataDefaults(g, attr = "count"), "class") = "INTEGER"
>> edgeDataDefaults(g, attr = "edgeType") = "undefined"
>> attr(edgeDataDefaults(g, attr = "edgeType"), "class") = "STRING"
>> # edgeDataDefaults(g, attr = "score") = 0
>> # attr(edgeDataDefaults(g, attr = "score"), "class") = "DOUBLE"
>> # edgeDataDefaults(g, attr = "misc") = ""
>> # attr(edgeDataDefaults(g, attr = "misc"), "class") = "STRING"
>> g = graph::addNode("A", g)
>> g = graph::addNode("B", g)
>> g = graph::addNode("C", g)
>> nodeData(g, "A", "type") = "kinase"
>> nodeData(g, "B", "type") = "transcription factor"
>> nodeData(g, "C", "type") = "glycoprotein"
>> nodeData(g, "A", "lfc") = "-3.0"
>> nodeData(g, "B", "lfc") = "0.0"
>> nodeData(g, "C", "lfc") = "3.0"
>> nodeData(g, "A", "count") = "2"
>> nodeData(g, "B", "count") = "30"
>> nodeData(g, "C", "count") = "100"
>> nodeData(g, "A", "label") = "Gene A"
>> nodeData(g, "B", "label") = "Gene B"
>> nodeData(g, "C", "label") = "Gene C"
>> g = graph::addEdge("A", "B", g)
>> g = graph::addEdge("B", "C", g)
>> g = graph::addEdge("C", "A", g)
>> # edgeData(g, "A", "B", "edgeType") = "phosphorylates"
>> # edgeData(g, "B", "C", "edgeType") = "synthetic lethal"
>> cw3 <- CytoscapeWindow("test3", graph=g, rpcPort=9000)
>> displayGraph(cw3)
> entering RCytoscape::displayGraph
> estimated displayGraph time: 15.1 seconds
> adding 3 nodes...
> sending 3 nodes
> ending sendNodes
> adding 3 edges...
> transforming (3) graph edges to nodePairTable
> sending 3 edges
> adding node attributes...
> [1] "type"
> [1] "lfc"
> [1] "label"
> [1] "count"
> adding edge attributes...
> [1] "edgeType"
> entering setEdgeAttributesDirect, edgeType, with 3 names and 3 values
> Error in file(file, ifelse(append, "a", "w")) :
> cannot open the connection
> In addition: Warning message:
> In file(file, ifelse(append, "a", "w")) :
> cannot open file 'data': Permission denied
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-pc-mingw32/x64 (64-bit)

> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> States.1252
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252

> attached base packages:
> [1] stats graphics grDevices utils datasets methods base

> other attached packages:
> [1] RCytoscape_1.7.11 XMLRPC_0.2-4 graph_1.35.1

> loaded via a namespace (and not attached):
> [1] BiocGenerics_0.3.0 RCurl_1.91-1.1 tools_2.15.0 XML_3.9-4.1
>> Sys.time()
> [1] "2012-07-23 10:38:05 EDT"

Robert M. Flight

View profile

More options Jul 23 2012, 11:36 am

From: "Robert M. Flight" <rfligh...@gmail.com>

Date: Mon, 23 Jul 2012 11:36:51 -0400

Local: Mon, Jul 23 2012 11:36 am

Subject: Re: RCy 1.7.11 edgeAttributes bug

Print | Individual message | Show original | Report this message | Find messages by this author

Hi Paul,

The results of traceback() are:

> traceback()

12: file(file, ifelse(append, "a", "w"))
11: cat(x, file = file, sep = c(rep.int(sep, ncolumns - 1), "\n"),
append = append)
10: write(sprintf("leaving setEdgeAttributesDirect"))
9: setEdgeAttributesDirect(obj, attribute.name,
caller.specified.attribute.class,
edge.names, values)
8: setEdgeAttributesDirect(obj, attribute.name,
caller.specified.attribute.class,
edge.names, values)
7: setEdgeAttributes(obj, name)
6: setEdgeAttributes(obj, name)
5: FUN("edgeType"[[1L]], ...)
4: lapply(X = X, FUN = FUN, ...)
3: sapply(eda.names(obj@graph), function(name) {
print(name)
setEdgeAttributes(obj, name)
})
2: displayGraph(cw3)
1: displayGraph(cw3)

It appears to be the point at which the edge attributes are appended
to the connection to Cy using "cat". Is there a bad value of "append"
there?

-Robert

On Mon, Jul 23, 2012 at 11:25 AM, Paul Shannon

- Show quoted text -

<paul.thurmond.shan...@gmail.com> wrote:
> Hi Robert,

> This is a mystery. I know of no call to append in RCytoscape. Could you call 'traceback ()' when the error occurs? That should reveal where the failed call is coming from.

> I checked in your improvements to "remove.redundancies.in.undirected.graph" on Saturday. They should show up as 1.17.12 by tomorrow morning.

> Looking forward to seeing what traceback () says --

> - Paul

> On Jul 23, 2012, at 7:40 AM, Robert M. Flight wrote:

>> In RCy 1.7.11, adding edge attributes causes a failure, in that the
>> attributes cannot be sent to the Cytoscape connection.

>> Examples below.

>> -Robert

>> Robert M. Flight, Ph.D.
>> robertmflight.blogspot.com
>> bioinformatics.louisville.edu/lab
>> github.com/rmflight/general/wiki

>> The most exciting phrase to hear in science, the one that heralds new
>> discoveries, is not "Eureka!" (I found it!) but "That's funny ..." -
>> Isaac Asimov

>>> options(save.defaults=list(compress="xz"), stringsAsFactors=FALSE)
>>> require(RCytoscape)
>> Loading required package: RCytoscape
>> Loading required package: graph
>> Loading required package: XMLRPC
>> Warning message:
>> package ‘RCytoscape’ was built under R version 2.15.1
>>> # note that is directly from Pauls 'makeSimpleGraph' function
>>> g = new("graphNEL", edgemode = "directed")
>>> nodeDataDefaults(g, attr = "type") = "undefined"
>>> attr(nodeDataDefaults(g, attr = "type"), "class") = "STRING"
>>> nodeDataDefaults(g, attr = "lfc") = 1
>>> attr(nodeDataDefaults(g, attr = "lfc"), "class") = "DOUBLE"
>>> nodeDataDefaults(g, attr = "label") = "default node label"
>>> attr(nodeDataDefaults(g, attr = "label"), "class") = "STRING"
>>> nodeDataDefaults(g, attr = "count") = "0"
>>> attr(nodeDataDefaults(g, attr = "count"), "class") = "INTEGER"
>>> edgeDataDefaults(g, attr = "edgeType") = "undefined"
>>> attr(edgeDataDefaults(g, attr = "edgeType"), "class") = "STRING"
>>> edgeDataDefaults(g, attr = "score") = 0
>>> attr(edgeDataDefaults(g, attr = "score"), "class") = "DOUBLE"
>>> edgeDataDefaults(g, attr = "misc") = ""
>>> attr(edgeDataDefaults(g, attr = "misc"), "class") = "STRING"
>>> g = graph::addNode("A", g)
>>> g = graph::addNode("B", g)
>>> g = graph::addNode("C", g)
>>> nodeData(g, "A", "type") = "kinase"
>>> nodeData(g, "B", "type") = "transcription factor"
>>> nodeData(g, "C", "type") = "glycoprotein"
>>> nodeData(g, "A", "lfc") = "-3.0"
>>> nodeData(g, "B", "lfc") = "0.0"
>>> nodeData(g, "C", "lfc") = "3.0"
>>> nodeData(g, "A", "count") = "2"
>>> nodeData(g, "B", "count") = "30"
>>> nodeData(g, "C", "count") = "100"
>>> nodeData(g, "A", "label") = "Gene A"
>>> nodeData(g, "B", "label") = "Gene B"
>>> nodeData(g, "C", "label") = "Gene C"
>>> g = graph::addEdge("A", "B", g)
>>> g = graph::addEdge("B", "C", g)
>>> g = graph::addEdge("C", "A", g)
>>> edgeData(g, "A", "B", "edgeType") = "phosphorylates"
>>> edgeData(g, "B", "C", "edgeType") = "synthetic lethal"
>>> edgeData(g, "A", "B", "score") = 35
>>> edgeData(g, "B", "C", "score") = -12
>>> cw1 <- CytoscapeWindow("test1", graph=g, rpcPort=9000)
>>> displayGraph(cw1)
>> entering RCytoscape::displayGraph
>> estimated displayGraph time: 15.1 seconds
>> adding 3 nodes...
>> sending 3 nodes
>> ending sendNodes
>> adding 3 edges...
>> transforming (3) graph edges to nodePairTable
>> sending 3 edges
>> adding node attributes...
>> [1] "type"
>> [1] "lfc"
>> [1] "label"
>> [1] "count"
>> adding edge attributes...
>> [1] "edgeType"
>> entering setEdgeAttributesDirect, edgeType, with 3 names and 3 values
>> Error in file(file, ifelse(append, "a", "w")) :
>> cannot open the connection
>> In addition: Warning message:
>> In file(file, ifelse(append, "a", "w")) :
>> cannot open file 'data': Permission denied
>>> g = new("graphNEL", edgemode = "directed")
>>> nodeDataDefaults(g, attr = "type") = "undefined"
>>> attr(nodeDataDefaults(g, attr = "type"), "class") = "STRING"
>>> nodeDataDefaults(g, attr = "lfc") = 1
>>> attr(nodeDataDefaults(g, attr = "lfc"), "class") = "DOUBLE"
>>> nodeDataDefaults(g, attr = "label") = "default node label"
>>> attr(nodeDataDefaults(g, attr = "label"), "class") = "STRING"
>>> nodeDataDefaults(g, attr = "count") = "0"
>>> attr(nodeDataDefaults(g, attr = "count"), "class") = "INTEGER"
>>> # edgeDataDefaults(g, attr = "edgeType") = "undefined"
>>> # attr(edgeDataDefaults(g, attr = "edgeType"), "class") = "STRING"
>>> # edgeDataDefaults(g, attr = "score") = 0
>>> # attr(edgeDataDefaults(g, attr = "score"), "class") = "DOUBLE"
>>> # edgeDataDefaults(g, attr = "misc") = ""
>>> # attr(edgeDataDefaults(g, attr = "misc"), "class") = "STRING"
>>> g = graph::addNode("A", g)
>>> g = graph::addNode("B", g)
>>> g = graph::addNode("C", g)
>>> nodeData(g, "A", "type") = "kinase"
>>> nodeData(g, "B", "type") = "transcription factor"
>>> nodeData(g, "C", "type") = "glycoprotein"
>>> nodeData(g, "A", "lfc") = "-3.0"
>>> nodeData(g, "B", "lfc") = "0.0"
>>> nodeData(g, "C", "lfc") = "3.0"
>>> nodeData(g, "A", "count") = "2"
>>> nodeData(g, "B", "count") = "30"
>>> nodeData(g, "C", "count") = "100"
>>> nodeData(g, "A", "label") = "Gene A"
>>> nodeData(g, "B", "label") = "Gene B"
>>> nodeData(g, "C", "label") = "Gene C"
>>> g = graph::addEdge("A", "B", g)
>>> g = graph::addEdge("B", "C", g)
>>> g = graph::addEdge("C", "A", g)
>>> # edgeData(g, "A", "B", "edgeType") = "phosphorylates"
>>> # edgeData(g, "B", "C", "edgeType") = "synthetic lethal"
>>> cw2 <- CytoscapeWindow("test2", graph=g, rpcPort=9000)
>>> displayGraph(cw2)
>> entering RCytoscape::displayGraph
>> estimated displayGraph time: 15.1 seconds
>> adding 3 nodes...
>> sending 3 nodes
>> ending sendNodes
>> adding 3 edges...
>> transforming (3) graph edges to nodePairTable
>> sending 3 edges
>> adding node attributes...
>> [1] "type"
>> [1] "lfc"
>> [1] "label"
>> [1] "count"
>> adding edge attributes...
>>> g = new("graphNEL", edgemode = "directed")
>>> nodeDataDefaults(g, attr = "type") = "undefined"
>>> attr(nodeDataDefaults(g, attr = "type"), "class") = "STRING"
>>> nodeDataDefaults(g, attr = "lfc") = 1
>>> attr(nodeDataDefaults(g, attr = "lfc"), "class") = "DOUBLE"
>>> nodeDataDefaults(g, attr = "label") = "default node label"
>>> attr(nodeDataDefaults(g, attr = "label"), "class") = "STRING"
>>> nodeDataDefaults(g, attr = "count") = "0"
>>> attr(nodeDataDefaults(g, attr = "count"), "class") = "INTEGER"
>>> edgeDataDefaults(g, attr = "edgeType") = "undefined"
>>> attr(edgeDataDefaults(g, attr = "edgeType"), "class") = "STRING"
>>> # edgeDataDefaults(g, attr = "score") = 0
>>> # attr(edgeDataDefaults(g, attr = "score"), "class") = "DOUBLE"
>>> # edgeDataDefaults(g, attr = "misc") = ""
>>> # attr(edgeDataDefaults(g, attr = "misc"), "class") = "STRING"
>>> g = graph::addNode("A", g)
>>> g = graph::addNode("B", g)
>>> g = graph::addNode("C", g)
>>> nodeData(g, "A", "type") = "kinase"
>>> nodeData(g, "B", "type") = "transcription factor"
>>> nodeData(g, "C", "type") = "glycoprotein"
>>> nodeData(g, "A", "lfc") = "-3.0"
>>> nodeData(g, "B", "lfc") = "0.0"
>>> nodeData(g, "C", "lfc") = "3.0"
>>> nodeData(g, "A", "count") = "2"
>>> nodeData(g, "B", "count") = "30"
>>> nodeData(g, "C", "count") = "100"
>>> nodeData(g, "A", "label") = "Gene A"
>>> nodeData(g, "B", "label") = "Gene B"
>>> nodeData(g, "C", "label") = "Gene C"
>>> g = graph::addEdge("A", "B", g)
>>> g = graph::addEdge("B", "C", g)
>>> g = graph::addEdge("C", "A", g)
>>> # edgeData(g, "A", "B", "edgeType") = "phosphorylates"
>>> # edgeData(g, "B", "C", "edgeType") = "synthetic lethal"
>>> cw3 <- CytoscapeWindow("test3", graph=g, rpcPort=9000)
>>> displayGraph(cw3)
>> entering RCytoscape::displayGraph
>> estimated displayGraph time: 15.1 seconds
>> adding 3 nodes...
>> sending 3 nodes
>> ending sendNodes
>> adding 3 edges...
>> transforming (3) graph edges to nodePairTable
>> sending 3 edges
>> adding node attributes...
>> [1] "type"
>> [1] "lfc"
>> [1] "label"
>> [1] "count"
>> adding edge attributes...
>> [1] "edgeType"
>> entering setEdgeAttributesDirect, edgeType, with 3 names and 3 values
>> Error in file(file, ifelse(append, "a", "w")) :
>> cannot open the connection
>> In addition: Warning message:
>> In file(file, ifelse(append, "a", "w")) :
>> cannot open file 'data': Permission denied
>>> sessionInfo()
>> R version 2.15.0 (2012-03-30)
>> Platform: x86_64-pc-mingw32/x64 (64-bit)

>> locale:
>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
>> States.1252
>> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252

>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base

>> other attached packages:
>> [1] RCytoscape_1.7.11 XMLRPC_0.2-4 graph_1.35.1

...

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Paul Shannon

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More options Jul 23 2012, 11:41 am

From: Paul Shannon <paul.thurmond.shan...@gmail.com>

Date: Mon, 23 Jul 2012 08:41:32 -0700

Local: Mon, Jul 23 2012 11:41 am

Subject: Re: RCy 1.7.11 edgeAttributes bug

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My dumb mistake in a residual trace statement.

write (sprintf ('format', args))

should be

write (sprintf ('format', args), stderr ())

If not given a specific argument (like stderr) apparently write () will write to 'data'.

I will fix this and update the repo. In the meantime, you can either delete the whole line, or add "stderr ()" as the last argument.

Sorry!

- Paul

On Jul 23, 2012, at 8:36 AM, Robert M. Flight wrote:

- Show quoted text -

> Hi Paul,

> The results of traceback() are:

>> traceback()
> 12: file(file, ifelse(append, "a", "w"))
> 11: cat(x, file = file, sep = c(rep.int(sep, ncolumns - 1), "\n"),
> append = append)
> 10: write(sprintf("leaving setEdgeAttributesDirect"))
> 9: setEdgeAttributesDirect(obj, attribute.name,
> caller.specified.attribute.class,
> edge.names, values)
> 8: setEdgeAttributesDirect(obj, attribute.name,
> caller.specified.attribute.class,
> edge.names, values)
> 7: setEdgeAttributes(obj, name)
> 6: setEdgeAttributes(obj, name)
> 5: FUN("edgeType"[[1L]], ...)
> 4: lapply(X = X, FUN = FUN, ...)
> 3: sapply(eda.names(obj@graph), function(name) {
> print(name)
> setEdgeAttributes(obj, name)
> })
> 2: displayGraph(cw3)
> 1: displayGraph(cw3)

> It appears to be the point at which the edge attributes are appended
> to the connection to Cy using "cat". Is there a bad value of "append"
> there?

> -Robert

> On Mon, Jul 23, 2012 at 11:25 AM, Paul Shannon
> <paul.thurmond.shan...@gmail.com> wrote:
>> Hi Robert,

>> This is a mystery. I know of no call to append in RCytoscape. Could you call 'traceback ()' when the error occurs? That should reveal where the failed call is coming from.

>> I checked in your improvements to "remove.redundancies.in.undirected.graph" on Saturday. They should show up as 1.17.12 by tomorrow morning.

>> Looking forward to seeing what traceback () says --

>> - Paul

>> On Jul 23, 2012, at 7:40 AM, Robert M. Flight wrote:

>>> In RCy 1.7.11, adding edge attributes causes a failure, in that the
>>> attributes cannot be sent to the Cytoscape connection.

>>> Examples below.

>>> -Robert

>>> Robert M. Flight, Ph.D.
>>> robertmflight.blogspot.com
>>> bioinformatics.louisville.edu/lab
>>> github.com/rmflight/general/wiki

>>> The most exciting phrase to hear in science, the one that heralds new
>>> discoveries, is not "Eureka!" (I found it!) but "That's funny ..." -
>>> Isaac Asimov

>>>> options(save.defaults=list(compress="xz"), stringsAsFactors=FALSE)
>>>> require(RCytoscape)
>>> Loading required package: RCytoscape
>>> Loading required package: graph
>>> Loading required package: XMLRPC
>>> Warning message:
>>> package ‘RCytoscape’ was built under R version 2.15.1
>>>> # note that is directly from Pauls 'makeSimpleGraph' function
>>>> g = new("graphNEL", edgemode = "directed")
>>>> nodeDataDefaults(g, attr = "type") = "undefined"
>>>> attr(nodeDataDefaults(g, attr = "type"), "class") = "STRING"
>>>> nodeDataDefaults(g, attr = "lfc") = 1
>>>> attr(nodeDataDefaults(g, attr = "lfc"), "class") = "DOUBLE"
>>>> nodeDataDefaults(g, attr = "label") = "default node label"
>>>> attr(nodeDataDefaults(g, attr = "label"), "class") = "STRING"
>>>> nodeDataDefaults(g, attr = "count") = "0"
>>>> attr(nodeDataDefaults(g, attr = "count"), "class") = "INTEGER"
>>>> edgeDataDefaults(g, attr = "edgeType") = "undefined"
>>>> attr(edgeDataDefaults(g, attr = "edgeType"), "class") = "STRING"
>>>> edgeDataDefaults(g, attr = "score") = 0
>>>> attr(edgeDataDefaults(g, attr = "score"), "class") = "DOUBLE"
>>>> edgeDataDefaults(g, attr = "misc") = ""
>>>> attr(edgeDataDefaults(g, attr = "misc"), "class") = "STRING"
>>>> g = graph::addNode("A", g)
>>>> g = graph::addNode("B", g)
>>>> g = graph::addNode("C", g)
>>>> nodeData(g, "A", "type") = "kinase"
>>>> nodeData(g, "B", "type") = "transcription factor"
>>>> nodeData(g, "C", "type") = "glycoprotein"
>>>> nodeData(g, "A", "lfc") = "-3.0"
>>>> nodeData(g, "B", "lfc") = "0.0"
>>>> nodeData(g, "C", "lfc") = "3.0"
>>>> nodeData(g, "A", "count") = "2"
>>>> nodeData(g, "B", "count") = "30"
>>>> nodeData(g, "C", "count") = "100"
>>>> nodeData(g, "A", "label") = "Gene A"
>>>> nodeData(g, "B", "label") = "Gene B"
>>>> nodeData(g, "C", "label") = "Gene C"
>>>> g = graph::addEdge("A", "B", g)
>>>> g = graph::addEdge("B", "C", g)
>>>> g = graph::addEdge("C", "A", g)
>>>> edgeData(g, "A", "B", "edgeType") = "phosphorylates"
>>>> edgeData(g, "B", "C", "edgeType") = "synthetic lethal"
>>>> edgeData(g, "A", "B", "score") = 35
>>>> edgeData(g, "B", "C", "score") = -12
>>>> cw1 <- CytoscapeWindow("test1", graph=g, rpcPort=9000)
>>>> displayGraph(cw1)
>>> entering RCytoscape::displayGraph
>>> estimated displayGraph time: 15.1 seconds
>>> adding 3 nodes...
>>> sending 3 nodes
>>> ending sendNodes
>>> adding 3 edges...
>>> transforming (3) graph edges to nodePairTable
>>> sending 3 edges
>>> adding node attributes...
>>> [1] "type"
>>> [1] "lfc"
>>> [1] "label"
>>> [1] "count"
>>> adding edge attributes...
>>> [1] "edgeType"
>>> entering setEdgeAttributesDirect, edgeType, with 3 names and 3 values
>>> Error in file(file, ifelse(append, "a", "w")) :
>>> cannot open the connection
>>> In addition: Warning message:
>>> In file(file, ifelse(append, "a", "w")) :
>>> cannot open file 'data': Permission denied
>>>> g = new("graphNEL", edgemode = "directed")
>>>> nodeDataDefaults(g, attr = "type") = "undefined"
>>>> attr(nodeDataDefaults(g, attr = "type"), "class") = "STRING"
>>>> nodeDataDefaults(g, attr = "lfc") = 1
>>>> attr(nodeDataDefaults(g, attr = "lfc"), "class") = "DOUBLE"
>>>> nodeDataDefaults(g, attr = "label") = "default node label"
>>>> attr(nodeDataDefaults(g, attr = "label"), "class") = "STRING"
>>>> nodeDataDefaults(g, attr = "count") = "0"
>>>> attr(nodeDataDefaults(g, attr = "count"), "class") = "INTEGER"
>>>> # edgeDataDefaults(g, attr = "edgeType") = "undefined"
>>>> # attr(edgeDataDefaults(g, attr = "edgeType"), "class") = "STRING"
>>>> # edgeDataDefaults(g, attr = "score") = 0
>>>> # attr(edgeDataDefaults(g, attr = "score"), "class") = "DOUBLE"
>>>> # edgeDataDefaults(g, attr = "misc") = ""
>>>> # attr(edgeDataDefaults(g, attr = "misc"), "class") = "STRING"
>>>> g = graph::addNode("A", g)
>>>> g = graph::addNode("B", g)
>>>> g = graph::addNode("C", g)
>>>> nodeData(g, "A", "type") = "kinase"
>>>> nodeData(g, "B", "type") = "transcription factor"
>>>> nodeData(g, "C", "type") = "glycoprotein"
>>>> nodeData(g, "A", "lfc") = "-3.0"
>>>> nodeData(g, "B", "lfc") = "0.0"
>>>> nodeData(g, "C", "lfc") = "3.0"
>>>> nodeData(g, "A", "count") = "2"
>>>> nodeData(g, "B", "count") = "30"
>>>> nodeData(g, "C", "count") = "100"
>>>> nodeData(g, "A", "label") = "Gene A"
>>>> nodeData(g, "B", "label") = "Gene B"
>>>> nodeData(g, "C", "label") = "Gene C"
>>>> g = graph::addEdge("A", "B", g)
>>>> g = graph::addEdge("B", "C", g)
>>>> g = graph::addEdge("C", "A", g)
>>>> # edgeData(g, "A", "B", "edgeType") = "phosphorylates"
>>>> # edgeData(g, "B", "C", "edgeType") = "synthetic lethal"
>>>> cw2 <- CytoscapeWindow("test2", graph=g, rpcPort=9000)
>>>> displayGraph(cw2)
>>> entering RCytoscape::displayGraph
>>> estimated displayGraph time: 15.1 seconds
>>> adding 3 nodes...
>>> sending 3 nodes
>>> ending sendNodes
>>> adding 3 edges...
>>> transforming (3) graph edges to nodePairTable
>>> sending 3 edges
>>> adding node attributes...
>>> [1] "type"
>>> [1] "lfc"
>>> [1] "label"
>>> [1] "count"
>>> adding edge attributes...
>>>> g = new("graphNEL", edgemode = "directed")
>>>> nodeDataDefaults(g, attr = "type") = "undefined"
>>>> attr(nodeDataDefaults(g, attr = "type"), "class") = "STRING"
>>>> nodeDataDefaults(g, attr = "lfc") = 1
>>>> attr(nodeDataDefaults(g, attr = "lfc"), "class") = "DOUBLE"
>>>> nodeDataDefaults(g, attr = "label") = "default node label"
>>>> attr(nodeDataDefaults(g, attr = "label"), "class") = "STRING"
>>>> nodeDataDefaults(g, attr = "count") = "0"
>>>> attr(nodeDataDefaults(g, attr = "count"), "class") = "INTEGER"
>>>> edgeDataDefaults(g, attr = "edgeType") = "undefined"
>>>> attr(edgeDataDefaults(g, attr = "edgeType"), "class") = "STRING"
>>>> # edgeDataDefaults(g, attr = "score") = 0
>>>> # attr(edgeDataDefaults(g, attr = "score"), "class") = "DOUBLE"
>>>> # edgeDataDefaults(g, attr = "misc") = ""
>>>> # attr(edgeDataDefaults(g, attr = "misc"), "class") = "STRING"
>>>> g = graph::addNode("A", g)
>>>> g = graph::addNode("B", g)
>>>> g = graph::addNode("C", g)
>>>> nodeData(g, "A", "type") = "kinase"
>>>> nodeData(g, "B", "type") = "transcription factor"
>>>> nodeData(g, "C", "type") = "glycoprotein"
>>>> nodeData(g, "A", "lfc") = "-3.0"
>>>> nodeData(g, "B", "lfc") = "0.0"
>>>> nodeData(g, "C", "lfc") = "3.0"
>>>> nodeData(g, "A", "count") = "2"
>>>> nodeData(g, "B", "count") = "30"
>>>> nodeData(g, "C", "count") = "100"
>>>> nodeData(g, "A", "label") = "Gene A"
>>>> nodeData(g, "B", "label") = "Gene B"
>>>> nodeData(g, "C", "label") = "Gene C"
>>>> g = graph::addEdge("A", "B", g)
>>>> g = graph::addEdge("B", "C", g)
>>>> g = graph::addEdge("C", "A", g)
>>>> # edgeData(g, "A", "B", "edgeType") = "phosphorylates"
>>>> # edgeData(g, "B", "C", "edgeType") = "synthetic lethal"
>>>> cw3 <- CytoscapeWindow("test3", graph=g, rpcPort=9000)
>>>> displayGraph(cw3)
>>> entering RCytoscape::displayGraph
>>> estimated displayGraph time: 15.1 seconds
>>> adding 3 nodes...
>>> sending 3 nodes
>>> ending sendNodes
>>> adding 3 edges...
>>> transforming (3) graph edges to nodePairTable
>>> sending 3 edges
>>> adding node attributes...
>>> [1] "type"
>>> [1] "lfc"
>>> [1] "label"
>>> [1] "count"
>>> adding edge attributes...
>>> [1] "edgeType"
>>> entering setEdgeAttributesDirect, edgeType, with 3 names and 3

...

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