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Question: Rcytoscape Rstudio Error in xml.rpc(obj@uri, "Cytoscape.version") : Problems
1
gravatar for alessandro brozzi
3.1 years ago by
European Union
alessandro brozzi120 wrote:

Dears,

I use Cytoscape 2.8 and Rcytoscape on my Ubuntu 64bit machine.

If I start an R session from the terminal and I run the following code:

library(RCytoscape)
g = new("graphNEL", edgemode="directed")
g = graph::addNode("U",g)
cw = new.CytoscapeWindow("vignette"

, graph=g, overwriteWindow=TRUE)
displayGraph(cw)

it works properly. Fine!

But the same code from Rstudio returns the following error:

> cw = new.CytoscapeWindow("vignette", graph=g, overwriteWindow=TRUE)
Error in xml.rpc(obj@uri, "Cytoscape.version") : Problems


Have you ever encountered this problem?

Thanks a lot for any hint!
Alessandro

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=it_IT.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] RCurl_1.95-4.3       bitops_1.0-6         RCytoscape_1.12.0
 [4] XMLRPC_0.3-0         graph_1.40.1         igraph_0.7.1
 [7] plyr_1.8.1           org.Hs.eg.db_2.10.1  RSQLite_0.11.4
[10] DBI_0.3.1            AnnotationDbi_1.24.0 Biobase_2.22.0
[13] BiocGenerics_0.8.0   BiocInstaller_1.12.1 intervals_0.15.0

loaded via a namespace (and not attached):
[1] IRanges_1.20.7 Rcpp_0.11.3    stats4_3.0.2   tools_3.0.2
XML_3.98-1.1

ADD COMMENTlink modified 3.0 years ago by drsuuzzz0 • written 3.1 years ago by alessandro brozzi120
0
gravatar for Andrzej Oleś
3.1 years ago by
Andrzej Oleś670
EMBL Heidelberg, Germany
Andrzej Oleś670 wrote:

Hi Alessandro,

can you please make sure that you're using the same versions of R and RCytoscape in both cases, i.e. the version numbers returned by sessionInfo() are the same in R run from terminal and in RStudio?

Best, Andrzej

ADD COMMENTlink written 3.1 years ago by Andrzej Oleś670
0
gravatar for alessandro brozzi
3.1 years ago by
European Union
alessandro brozzi120 wrote:

hi Andrzej,

yes the session info are exactley the same.

In th epast days did a lot of debugging. What I guess is something wrong here:

> xml.rpc(cy.tmp,"Cytoscape.version")
Error in .postForm(curl, .opts, .params, style) :
  Unhandled case for the value of curl_easy_setopt (R type = 25, option 10002)

my two cents,

Alex

 

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=it_IT.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] RCytoscape_1.12.0 XMLRPC_0.3-0      graph_1.40.1     

loaded via a namespace (and not attached):
[1] BiocGenerics_0.8.0 parallel_3.0.2     RCurl_1.95-4.3    
[4] stats4_3.0.2       tools_3.0.2        XML_3.98-1.1  

ADD COMMENTlink written 3.1 years ago by alessandro brozzi120
0
gravatar for Andrzej Oleś
3.1 years ago by
Andrzej Oleś670
EMBL Heidelberg, Germany
Andrzej Oleś670 wrote:

Hi Alex,

I don't know whether this is useful for you, but I tried to reproduce your issue by installing Cytoscape 2.8.1 along with the CytoscapeRPC plugin from http://apps.cytoscape.org .

Interestingly, when trying to run your example I get the following error (both from console and RStudio):

> library(RCytoscape)
> g = new("graphNEL", edgemode="directed")
> g = graph::addNode("U",g)
> cw = new.CytoscapeWindow("vignette", graph=g, overwriteWindow=TRUE)
nodes have no label attribute -- adding default labels
> displayGraph(cw)
estimated displayGraph time:      0.0 seconds
adding 1 nodes...
sending 1 nodes
Error: faultCode:  0  faultString:  No method matching arguments: java.lang.String, java.lang.String

The example from the RCytoscape vignette

> library(RCytoscape)
> g <- new ('graphNEL', edgemode='directed')
> g <- graph::addNode ('A', g)
> g <- graph::addNode ('B', g)
> g <- graph::addNode ('C', g)
> cw <- new.CytoscapeWindow ('vignette', graph=g)
> displayGraph (cw)

works just fine for me, both from terminal and RStudio.

What I've noticed is that you're using an outdated version of R (3.0.2 vs. 3.1.1). Also, what version of Cytoscape are you using exactly?

Best,

Andrzej

ADD COMMENTlink written 3.1 years ago by Andrzej Oleś670
0
gravatar for pshannon
3.1 years ago by
pshannon80
United States
pshannon80 wrote:

The "no method matching arguments: java.lang.String, java.lang.String" for a 1-node graph gives us the clue we need -- and points to my programming bug.

In R, even a scalar is a list, but when translated to XML and then java, a scalar is a scalar.

It appears therefore that I never tested a 1-node graph, and you walked right into my omission.

Thanks to Andrzej for pointing out the 3-node example, and offering the suggestion to upgrade your R to 3.1.1.

RCytoscape works only with versions 2.x of Cytoscape, with 2.8.3 strongly recommended.  We have a volunteer working on porting RCytoscape to versions >-= 3.2,  and I am (slowly) doing the port to cytoscape.js.

I will fix the current release and devel versions of RCy to handle 1-node graphs.

 - Paul

ADD COMMENTlink written 3.1 years ago by pshannon80
0
gravatar for alessandro brozzi
3.1 years ago by
European Union
alessandro brozzi120 wrote:

hi!

Thank you very much for the suggestions.

I made the R upgrade but the error is still there :( I don't really understand why from the console it perfectly works.

May be due to some "proxy" configurations?

BTW: Cytoscape rel: 2.8.3, plugin: 1.8

bests!

Alex

ADD COMMENTlink written 3.1 years ago by alessandro brozzi120
0
gravatar for pshannon
3.1 years ago by
pshannon80
United States
pshannon80 wrote:

Hi Alex,

Sorry you are still having trouble with RStudio/RCy.   In your original posting -- forgive me if you provided more information and I missed it --you say:

> cw = new.CytoscapeWindow("vignette", graph=g, overwriteWindow=TRUE)
Error in xml.rpc(obj@uri, "Cytoscape.version") : Problems

Can you provide the full traceback (via the "traceback()" command)?

For what it's worth, I just installed the latest RStudio, started up Cytoscape 2.8.3:

library(RCytoscape)
demoSimpleGraph()

and everything worked fine.    

With more details, we should be able to figure out your problem.

- Paul

ADD COMMENTlink written 3.1 years ago by pshannon80
0
gravatar for alessandro brozzi
3.1 years ago by
European Union
alessandro brozzi120 wrote:

hi Paul,

fisrt of all thank you sincerely for the help you are providing.

Here we go:

> cw = new.CytoscapeWindow('vignette', graph=g, overwriteWindow=TRUE)
Error in xml.rpc(obj@uri, "Cytoscape.version") : Problems
> traceback()
6: stop("Problems")
5: xml.rpc(obj@uri, "Cytoscape.version")
4: pluginVersion(cyCon)
3: pluginVersion(cyCon)
2: check.cytoscape.plugin.version(cy.tmp)
1: new.CytoscapeWindow("vignette", graph = g, overwriteWindow = TRUE)

(RStudio Version: 0.98.1049)

demoSimpleGraph() works fine from the console but again not from RStudio.

HTH,

Alex

ADD COMMENTlink written 3.1 years ago by alessandro brozzi120
0
gravatar for pshannon
3.1 years ago by
pshannon80
United States
pshannon80 wrote:

Hi Alex,

Try this:

library(RCytoscape)
cw = new.CytoscapeWindow ("test", graph=RCytoscape::makeSimpleGraph ())
xml.rpc(cw@uri, "Cytoscape.test")  #  should display   [1] "It works!"

- Paul

ADD COMMENTlink written 3.1 years ago by pshannon80
0
gravatar for alessandro brozzi
3.1 years ago by
European Union
alessandro brozzi120 wrote:

hi paul,

> library(RCytoscape)
Loading required package: graph
Loading required package: XMLRPC
> cw = new.CytoscapeWindow ("test", graph=RCytoscape::makeSimpleGraph ())
Error in xml.rpc(obj@uri, "Cytoscape.version") : Problems
> xml.rpc(cw@uri, "Cytoscape.test")
Error in merge(list(...), .opts) : object 'cw' not found

don't worry I'll find another solution. In any computer I had it was working. It might simply be a problem with this machine.

alex

ADD COMMENTlink written 3.1 years ago by alessandro brozzi120
0
gravatar for pshannon
3.1 years ago by
pshannon80
United States
pshannon80 wrote:

HI Alex,

I suspect you are right:  some port blocked, perhaps.

Here is a simple no-Cytoscape test which may be useful:

 

url <- "http://xmlrpc-c.sourceforge.net/api/sample.php"
xml.rpc (url, 'sample.add', 1L, 1L)  # [1] 2

- Paul

 

ADD COMMENTlink written 3.1 years ago by pshannon80
0
gravatar for drsuuzzz
3.0 years ago by
drsuuzzz0
United States
drsuuzzz0 wrote:

Hi,

I'm having the same problem with R 3.1.2 and Cytoscape 2.8.3 on Windows 7.  I see the problem on the command line and within R studio.However, I get a different error when attempting demoSimpleGraph().  Is there any news on a work around?

Thanks!

Suzy

> library(RCytoscape)
Loading required package: graph
Loading required package: XMLRPC
> demoSimpleGraph()
Error in xml.rpc(obj@uri, "Cytoscape.getNetworkCount") : Problems
> traceback()
9: stop("Problems")
8: xml.rpc(obj@uri, "Cytoscape.getNetworkCount")
7: getWindowCount(obj)
6: getWindowCount(obj)
5: getWindowList(cy)
4: getWindowList(cy)
3: match(x, table, nomatch = 0L)
2: window.title %in% as.character(getWindowList(cy))
1: demoSimpleGraph()

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] 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_1.16.0 XMLRPC_0.3-0      graph_1.44.0

loaded via a namespace (and not attached):
[1] BiocGenerics_0.12.1 parallel_3.1.2      RCurl_1.95-4.3
[4] stats4_3.1.2        tools_3.1.2         XML_3.98-1.1

ADD COMMENTlink written 3.0 years ago by drsuuzzz0

hi,

I solved it setting no http proxy:

Sys.setenv(http_proxy="")

HTH

alex

 

 

ADD REPLYlink written 2.9 years ago by alessandro brozzi120
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